Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice

Grain size and shape are important components determining rice grain yield, and they are controlled by quantitative trait loci (QTLs). Here, we report the cloning and functional characterization of a major grain length QTL, qGL3, which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of the qgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties, due to its favorable effect on grain length, filling, and weight.     

Suppressed expression of RETROGRADE-REGULATED MALE STERILITY restores pollen fertility in cytoplasmic male sterile rice plants

Conflict/reconciliation between mitochondria and nuclei in plants is manifested by the fate of pollen (viable or nonviable) in the cytoplasmic male sterility (CMS)/fertility restoration (Rf) system. Through positional cloning, we identified a nuclear candidate gene, RETROGRADE-REGULATED MALE STERILITY (RMS) for Rf17, a fertility restorer gene for Chinese wild rice (CW)-type CMS in rice (Oryza sativa L.). RNA interference-mediated gene silencing of RMS restored fertility to a CMS plant, whereas its overexpression in the fertility restorer line induced pollen abortion. The mRNA expression level of RMS in mature anthers depended on cytoplasmic genotype, suggesting that RMS is a candidate gene to be regulated via retrograde signaling. We found that a reduced-expression allele of the RMS gene restored fertility in haploid pollen, whereas a normal-expression allele caused pollen to die in the CW-type CMS. RMS encodes a mitochondrial protein, 178 aa in length, of unknown function, unlike the majority of other Rf genes cloned thus far, which encode pentatricopeptide repeat proteins. The unique features of RMS provide novel insights into retrograde signaling and CMS.     

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang–You–Pei–Jiu, the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93–11 and maternal cultivar PA64s of Liang–You–Pei–Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1, and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice.Rice is one of the most important staple crops in the world and serves as a model for monocots (1). Currently, rice breeding faces the challenge of overcoming the yield plateau. All important agronomic traits would ultimately need to consider their impacts on the yield, which is linked to various growth and developmental components, such as tiller number, seed number and set, and grain weight, to name a few. A number of quantitative trait loci (QTLs) have been reported to control these components, including those revealed by map-based cloning studies, such as IPA1/WFP for tiller and spikelet numbers (2, 3); days to heading8 (DTH8)/Ghd8 and Ghd7 for heading date, plant height, and spikelet number (4, 5); Gn1 for spikelet number (6); GIF1 for seed set (7); and grain size3 (GS3) and GW5 for grain size and weight (8, 9). Although a series of QTLs for yield components have been cloned, elucidation of the genetic mechanisms underlying the inheritance of superior yield in super hybrid rice still has a long way to go.Hybrid rice has a notable contribution to yield improvement. Various commercialized hybrids are derived by crossing different varieties within or between two subspecies, Oryza sativa ssp. indica and ssp. japonica (10, 11). As a pioneer super hybrid rice, Liang–You–Pei–Jiu (LYP9) realized the target of 10.5 tons/ha in 2000 (12). LYP9 was developed by a cross of the paternal 93–11, an indica variety widely grown in China (13), and the maternal PA64s cultivar with a mixed genetic background of indica and javanica. To date, it has been widely cultivated for commercial production in China. Such a feature was thought to make LYP9 recombinant inbred lines (RILs) ideal materials for exploring molecular mechanisms underlying rice yield.Here, we constructed a high-density linkage map by resequencing the parents of LYP9 and 132 core RILs. As a result, we finished the chromosome-scale genome sequence of PA64s and updated the 93–11 genome sequence by anchoring to chromosomes, filling up gaps, and correcting single-base errors. Twenty-five unique QTLs related to rice production were identified. One QTL, qSN8 for spikelet number, was fine-mapped with a large RIL population and confirmed as DTH8 by a complementation test.     

Clinically relevant RHD-CE genotypes in patients with sickle cell disease and in African Brazilian donors

BackgroundAs a consequence of the homology and opposite orientation of RHD and RHCE, numerous gene rearrangements have occurred in Africans and resulted in altered RH alleles that predict partial antigens, contributing to the high rate of Rh alloimmunisation among patients with sickle cell disease (SCD). In this study, we characterised variant RH alleles encoding partial antigens and/or lacking high prevalence antigens in patients with SCD and in African Brazilian donors, in order to support antigen-matched blood for transfusion.ResultsThe distributions of RHD and RHCE alleles in donors and patients were similar. We found RHCE variant alleles inherited with altered RHD alleles in 25 out of 168 patients (15%) and in 22 out of 280 (7.8%) African Brazilian donors. The RHD and RHCE allele combinations found in the population studied were: RHD*DAR with RHCE*ceAR; RHD*weak D type 4.2.2 with RHCE*ceAR, RHD*weak D type 4.0 with RHCE*ceVS.01 and RHCE*ceVS.02; RHD*DIIIa with RHCE*ceVS.02. Thirteen patients and six donors had RHD-CE genotypes with homozygous or compound heterozygous alleles predicting partial antigens and/or lacking high prevalence antigens. Eleven patients were alloimmunised to Rh antigens. For six patients with RHD-CE genotypes predicting partial antigens, no donors with similar genotypes were found.DiscussionKnowledge of the distribution and prevalence of RH alleles in patients with SCD and donors of African origin may be important for implementing a programme for RH genotype matching in SCD patients with RH variant alleles and clinically significant Rh antibodies.     

Archaeological and genetic insights into the origins of domesticated rice

Rice (Oryza sativa) is one of the most important cereal grains in the world today and serves as a staple food source for more than half of the world’s population. Research into when, where, and how rice was brought into cultivation and eventually domesticated, along with its development into a staple food source, is thus essential. These questions have been a point of nearly continuous research in both archaeology and genetics, and new information has continually come to light as theory, data acquisition, and analytical techniques have advanced over time. Here, we review the broad history of our scientific understanding of the rice domestication process from both an archaeological and genetic perspective and examine in detail the information that has come to light in both of these fields in the last 10 y. Current findings from genetics and archaeology are consistent with the domestication of O. sativa japonica in the Yangtze River valley of southern China. Interestingly, although it appears rice was cultivated in the area by as early 8000 BP, the key domestication trait of nonshattering was not fixed for another 1,000 y or perhaps longer. Rice was also cultivated in India as early as 5000 BP, but the domesticated indica subspecies currently appears to be a product of the introgression of favorable alleles from japonica. These findings are reshaping our understanding of rice domestication and also have implications for understanding the complex evolutionary process of plant domestication.     

NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars

Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13–36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.The world’s population is expected to surpass 9 billion in 2050 (http://esa.un.org/unpd/ppp/index.htm). Most of this increase will occur in the developing countries of Asia and Africa. By 2035, a 26% increase in rice production will be essential to feed the rising population (1, 2). Rice (Oryza sativa L.) is a staple food of more than 3 billion people, mainly in Asia. Predominantly, indica cultivars are grown in southern China, Southeast Asia, and South Asia, occupying approximately 70% of the rice-producing area in the world, whereas japonica cultivars are grown mainly in East Asia (3, 4). Because of urbanization and industrialization, an increase in the yield of indica cultivars is a pressing need in Southeast and South Asia (5). Additionally, good grain quality (influencing market value) and high yield are essential for the adoption of new cultivars in local areas (6).The grain yield of rice is determined by spikelet number per panicle, panicle number per plant, grain weight, and spikelet fertility. Although many quantitative trait loci (QTLs) for yield components have been identified (www.gramene.org), few have so far been isolated. To date, at least nine genes or loci for yield-related traits in rice have been isolated from natural variation: Gn1a and APO1 for number of grains (7–9); GS3, GW2, and qSW5 for grain size (10–12); DEP1 and WFP for panicle architecture (13, 14); SCM2 for strong culm (15); and Ghd7 for late heading and number of grains (16). APO1, SCM2, and DEP1 increased grain yield in a japonica genetic background in field experiments (9, 13, 15). However, no novel cloned gene has been reported to increase grain yield in indica cultivars (17). Here, we identified a gene in a tropical japonica landrace and used the allele to increase the grain yield of modern indica cultivars at the crop level through a breeding concept developed by International Rice Research Institute (IRRI) breeders more than 20 y ago.In 1989, a breeding program for New Plant Type (NPT) rice was launched at IRRI to increase the yields of modern indica cultivars by using genetic material from tropical japonica landraces (18). Several Indonesian tropical japonica landraces—which are characterized by large panicles, large leaves, a vigorous root system, thick stems, and few unproductive tillers—have been used in international breeding programs. However, despite these features, the NPT cultivars yield less than modern indica cultivars, mainly because of low grain fertility and low panicle number (19, 20). To genetically dissect and elicit the valuable traits of NPT cultivars, we backcrossed the NPT cultivars including YP9 (IR68522-10-2-2) against modern indica cultivar IR64 to develop introgression lines (ILs) (Fig. S1). BC₃-derived ILs, which had favorable yield-related traits and few undesirable traits, were selected by field observation (21). Using the ILs, we identified 21 QTLs for yield components such as total spikelet number per panicle (TSN), grain weight, and panicle number. Among the QTLs, qTSN4, for high TSN, was commonly detected on the long arm of chromosome 4 in five NPT lines derived from different tropical japonica cultivars (22). Additionally, a near-isogenic line (NIL) for qTSN4 from YP9, derived from tropical japonica landrace Daringan with an IR64 genetic background, had more spikelets per panicle and more branches than IR64.In this study, we isolated the gene for qTSN4 through map-based cloning to facilitate its use in breeding. The phenotypic effects of the gene were validated in transgenic plants and by expression analysis. To confirm the effect on practical grain yield in the field, we evaluated yield and related traits by using NILs with genetic backgrounds of popular indica cultivars.     

Amino acid polymorphisms altering the glycosylation of IL-2 do not protect from type 1 diabetes in the NOD mouse

Idd3 is one of many gene regions that affect the development of type 1 diabetes (T1D) in the nonobese diabetic (NOD) mouse. Idd3 has been localized to a 650-kb region on chromosome 3 containing the IL-2 gene. Exon 1 of the IL-2 gene is polymorphic between the susceptible NOD and the protective C57BL/6 (B6) alleles, causing multiple amino acid changes that have been proposed to be responsible for the differing glycosylation status. To address whether this coding polymorphism recapitulates the disease suppression mediated by the B6 Idd3 allele, we generated knockin mice in which exon 1 of the B6 IL-2 allele replaces the homologous region in the NOD allele. We generated these mice by targeting the NOD allele of NOD/129 F₁ ES cells. IL-2 protein from the knockin mice showed the glycosylation pattern of the B6 IL-2 isoform, confirming that the amino acid differences encoded within exon 1 affect the glycosylation of the IL-2 protein. However, unlike NOD.B6 Idd3 congenic mice, the knockin mice were not protected from T1D. Furthermore, the difference in amino acid sequence in the IL-2 protein did not affect the level of expression of IL-2. This approach provides a general method for the determination of a functional role of a given genomic sequence in a disease process. Further, our result demonstrates that the variants in exon 1 of the IL-2 gene are not responsible for T1D suppression in NOD.B6 Idd3 mice, thereby supporting the hypothesis that variants in the regulatory region affecting expression levels are causative.     

Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution dwarf alleles in rice and barley

Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5), which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis, are found in different populations from southern, western, and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection, whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu’s H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore, because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes, this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants.Bioactive gibberellins (GAs) are plant growth regulators involved in important traits such as seed germination, flowering time, flower development, and elongation growth (1). GA biosynthesis and signaling pathways are well defined (1, 2) and have been targeted in crop breeding. Modification of GA pathways was crucial in the green revolution because it conferred semidwarfness, thus reducing lodging and increasing crop yields (3–6). Green revolution semidwarf varieties in wheat are due to mutations in DELLA genes, whereas many short straw rice varieties carry a mutation in the Semi-Dwarf-1 (SD1) locus. This locus codes for GA 20-oxidase-2, a GA biosynthesis gene that is also mutated in most modern barley varieties in which the gene was called Denso or Semi-dwarf 1 (Sdw1) (7).GA 20-oxidases are involved in the later steps of GA biosynthesis and belong to the group of 2-oxoglutarate–dependent dioxygenases that, together with GA 3-oxidases, form biologically active GA (8). Arabidopsis thaliana has five GA20ox paralogous genes. AtGA20ox-1, AtGA20ox-2, AtGA20ox-3, and AtGA20ox-4 can catalyze the in vitro conversion of GA₁₂ to GA₉. Therefore, GA20ox paralogs might have partial redundant functions (9). However, among paralog genes, only AtGA20ox-1 (GA5), which was cloned on the basis of the ga5 mutant (10), affected plant height (8).Natural variation for GA biosynthesis has been previously described in A. thaliana because the Bur-0 accession carries a loss-of-function allele at GA20ox4 (9), which does not result in a semidwarf phenotype. In addition, genetic variation in GA1 has been associated with variation in floral morphology (11). Furthermore, the semidwarf phenotype (here defined as a plant height shorter than half the size of genetically related individuals) observed in the Kas-2 accession is due to a recessive allele at the GA5 locus (12). The latter finding led to the questions of whether green revolution alleles, artificially selected in cereals, could also occur in natural populations of the wild species A. thaliana, and if so, how many different GA5 loss-of-function alleles exist, how they are distributed, and why they occur in some populations.     

Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers

The objective of the present study was to make use of efficient molecular marker systems to reveal genetic relationships in traditional and evolved Basmati (EB) and semidwarf non-Basmati (NB) rice varieties. A subset of three rice groups was analyzed by using 19 simple sequence repeat (SSR) loci and 12 inter-SSR-PCR primers. A total of 70 SSR alleles and 481 inter-SSR-PCR markers were revealed in 24 varieties from the three groups. The lowest genetic diversity was observed among the traditional Basmati varieties, whereas the EB varieties showed the highest genetic diversity by both the marker assays. The results indicated that the subset of aromatic rice varieties analyzed in the present study is probably derived from a single land race. The traditional Basmati (TB) and semidwarf NB rice varieties used in the present study were clearly delineated by both marker assays. A number of markers, which could unambiguously distinguish the TB varieties used in the present study from the evolved and NB rice varieties, were identified. The potential use of these markers in Basmati rice-breeding programs and authentication of TB varieties used in the present study are envisaged.     

A hyperactive quantitative trait locus allele of Arabidopsis BRX contributes to natural variation in root growth vigor

Quantitative trait loci analysis of natural Arabidopsis thaliana accessions is increasingly exploited for gene isolation. However, to date this has mostly revealed deleterious mutations. Among them, a loss-of-function allele identified the root growth regulator BREVIS RADIX (BRX). Here we present evidence that BRX and the paralogous BRX-LIKE (BRXL) genes are under selective constraint in monocotyledons as well as dicotyledons. Unexpectedly, however, whereas none of the Arabidopsis orthologs except AtBRXL1 could complement brx null mutants when expressed constitutively, nearly all monocotyledon BRXLs tested could. Thus, BRXL proteins seem to be more diversified in dicotyledons than in monocotyledons. This functional diversification was correlated with accelerated rates of sequence divergence in the N-terminal regions. Population genetic analyses of 30 haplotypes are suggestive of an adaptive role of AtBRX and AtBRXL1. In two accessions, Lc-0 and Lov-5, seven amino acids are deleted in the variable region between the highly conserved C-terminal, so-called BRX domains. Genotyping of 42 additional accessions also found this deletion in Kz-1, Pu2-7, and Ws-0. In segregating recombinant inbred lines, the Lc-0 allele (AtBRX^Lc-0) conferred significantly enhanced root growth. Moreover, when constitutively expressed in the same regulatory context, AtBRX^Lc-0 complemented brx mutants more efficiently than an allele without deletion. The same was observed for AtBRXL1, which compared with AtBRX carries a 13 amino acid deletion that encompasses the deletion found in AtBRX^Lc-0. Thus, the AtBRX^Lc-0 allele seems to contribute to natural variation in root growth vigor and provides a rare example of an experimentally confirmed, hyperactive allelic variant.     

The silkworm Green b locus encodes a quercetin 5-O-glucosyltransferase that produces green cocoons with UV-shielding properties

In the silkworm Bombyx mori, dietary flavonoids are metabolized and accumulate in cocoons, thereby causing green coloration. Classical genetic studies suggest that more than seven independent loci are associated with this trait; however, because of the complex inheritance pattern, none of these loci have been characterized molecularly, and a plausible and comprehensive model for their action has not been proposed. Here, we report the identification of the gene responsible for the Green b (Gb) locus involving the green cocoon trait. In +^Gb animals, glucosylation at the 5-O position of dietary quercetin did not occur, and the total amount of flavonoids in tissues and cocoons was dramatically reduced. We performed positional cloning of Gb and found a 38-kb deletion in a UDP-glucosyltransferase (UGT) gene cluster associated with the +^Gb allele. RT-PCR and biochemical studies suggested that deletion of Bm-UGT10286 (UGT) is responsible for Gb and Bm-UGT10286 is virtually the sole source of UGT activity toward the 5-O position of quercetin. Our data show that the regiospecific glucosylation of flavonoids by the quercetin 5-O-glucosyltransferase can greatly affect the overall bioavailability of flavonoids in animals. Furthermore, we provide evidence that flavonoids increase the UV-shielding activity of cocoons and thus could confer an increased survival advantage to insects contained in these cocoons. This study will lead to greater understanding of mechanisms for metabolism, uptake, and transport of dietary flavonoids, which have a variety of biological activities in animals and beneficial effects on human health.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:Geographic patterns of Plasmodium falciparum drug resistance distinguished by differential responses to amodiaquine and chloroquine

Chloroquine (CQ) resistance (CQR) in Plasmodium falciparum originated from at least six foci in South America, Asia, and Oceania. Malaria parasites from these locations exhibit contrasting resistance phenotypes that are distinguished by point mutations and microsatellite polymorphisms in and near the CQR transporter gene, pfcrt, and the multidrug resistance transporter gene, pfmdr1. Amodiaquine (AQ), a 4-aminoquinoline related to CQ, is recommended and often used successfully against CQ-resistant P. falciparum in Africa, but it is largely ineffective across large regions of South America. The relationship of different pfcrt and pfmdr1 combinations to these drug-resistant phenotypes has been unclear. In two P. falciparum genetic crosses, particular pfcrt and pfmdr1 alleles from South America interact to yield greater levels of resistance to monodesethylamodiaquine (MDAQ; the active metabolite of AQ) than to CQ, whereas a pfcrt allele from Southeast Asia and Africa is linked to greater CQ than MDAQ resistance with all partner pfmdr1 alleles. These results, together with (i) available haplotype data from other parasites; (ii) evidence for an emerging focus of AQ resistance in Tanzania; and (iii) the persistence of 4-aminoquinoline-resistant parasites in South America, where CQ and AQ use is largely discontinued, suggest that different histories of drug use on the two continents have driven the selection of distinct suites of pfcrt and pfmdr1 mutations. Increasing use of AQ in Africa poses the threat of a selective sweep of highly AQ-resistant, CQ-resistant parasites with pfcrt and pfmdr1 mutations that are as advantaged and persistent as in South America.     

Association between chloroquine resistance phenotypes and point mutations in pfcrt and pfmdr1 in Plasmodium falciparum isolates from Thailand

The relationship between the in vitro susceptibility of Plasmodium falciparum isolates to the quinoline antimalarials chloroquine (CQ), mefloquine (MQ), and quinine (QN), and pfcrt and pfmdr1 gene polymorphisms were investigated. Field isolates (110 samples) were collected from various endemic areas of Thailand throughout 2002-2004. The pfcrt 76T allele was identified in 109 isolates (99.1%) while pfcrt 76K was found in a single (0.9%) isolate. The pfmdr 86N, 86Y, and the combination (86N + 86Y) alleles were identified in 83 (75.5%), 22 (20%), and 5 (4.5%) isolates, respectively. The pfmdr1 1042N, 1042D alleles and a mixture (1042N + 1042D) of the alleles were found in 94 (85.5%), 12 (10.9%) and 4 (3.6%) isolates, respectively. The pfmdr1 1246Y allele was detected in a single (0.9%) isolate. The pfmdr1 gene polymorphisms (86-1042-1246) was grouped into seven haplotypes as follows: N-N-D (68 isolates; 61.2%), Y-N-D (22 isolates; 19.8%), N-D-D (11 isolates; 9.9%), N-D-Y (1 isolate; 0.9%), N/Y-N-D (4 isolates; 3.6%), N-N/D-D (3 isolates; 2.7%), and N/Y-N/D-D (1 isolate; 0.9%). Eight different combinations of pfcrt-pfmdr1 genotypes were observed. Only one CQ-, MQ- and QN-sensitive isolate was found at the Thai-Laos border and no cases of QN resistance were found in this study.     

Genetic Variants in the SAMM50 Gene Create Susceptibility to Nonalcoholic Fatty Liver Disease in a Chinese Han Population

Background:

Genome-wide association studies have shown that rs738491, rs2143571, and rs3761472 in the sorting and assembly machinery component 50 homolog (SAMM50) gene are significantly associated with susceptibility to nonalcoholic fatty liver disease (NAFLD).

Objectives:

The present study evaluated the association between the three genetic variants in the SAMM50 gene and susceptibility to NAFLD in a Chinese Han population.

Patients and Methods:

Genotypes for 3 single nucleotide polymorphisms (SNPs), viz rs738491, rs2143571, and rs3761472, in the SAMM50 gene were determined using an improved multiplex ligation detection reaction technique in 340 B-type ultrasonography-diagnosed NAFLD patients and 452 healthy controls. Meanwhile, serum lipid profiles and liver enzymes were estimated using standard clinical laboratory methods. The SNP-SNP interactions were analyzed by performing multifactor dimensionality reduction (MDR) and generalized multifactor dimensionality reduction (GMDR).

Results:

The genotype and allele frequencies of the SAMM50 polymorphisms between the NAFLD group and the control group were significantly different (all Ps < 0.05). In the multivariate analysis adjusted for gender, age, and body mass index, the carriers of the rs738491 T allele, rs2143571 A allele, and rs3761472 G allele had significantly increased susceptibility to NAFLD (OR, 1.507; 95% CI, 1.035 to 2.195; P = 0.032; OR, 1.761; 95% CI, 1.232 to 2.517; P = 0.002; OR, 1.483; 95% CI, 1.039 to 2.115; P = 0.030, respectively). Moreover, the rs738491 T allele carriers had significantly higher levels of alanine aminotransferase (ALT) (P = 0.017) than did the noncarriers. However, differences in the levels of serum triglyceride (TG) and aspartate aminotransferase (AST) were not statistically significant (P = 0.123; P = 0.107). The Rs2143571 A allele and the rs3761472 G allele were both deeply associated with increased levels of serum TG, ALT, and AST (all Ps < 0.05). Furthermore, the MDR and GMDR showed that a synergistic relationship might exist between rs738491, rs2143571, and rs3761472 in the SAMM50 gene and the pathophysiology and genetics of NAFLD.

Conclusions:

We first demonstrated that the rs738491 T allele, rs2143571 A allele, and rs3761472 G allele in the SAMM50 gene created susceptibility to NAFLD in a Chinese Han population. The combination of the three SNPs in the SAMM50 gene may have synergism to predict the predisposition to NAFLD.     

Activation of Big Grain1 significantly improves grain size by regulating auxin transport in rice

Grain size is one of the key factors determining grain yield. However, it remains largely unknown how grain size is regulated by developmental signals. Here, we report the identification and characterization of a dominant mutant big grain1 (Bg1-D) that shows an extra-large grain phenotype from our rice T-DNA insertion population. Overexpression of BG1 leads to significantly increased grain size, and the severe lines exhibit obviously perturbed gravitropism. In addition, the mutant has increased sensitivities to both auxin and N-1-naphthylphthalamic acid, an auxin transport inhibitor, whereas knockdown of BG1 results in decreased sensitivities and smaller grains. Moreover, BG1 is specifically induced by auxin treatment, preferentially expresses in the vascular tissue of culms and young panicles, and encodes a novel membrane-localized protein, strongly suggesting its role in regulating auxin transport. Consistent with this finding, the mutant has increased auxin basipetal transport and altered auxin distribution, whereas the knockdown plants have decreased auxin transport. Manipulation of BG1 in both rice and Arabidopsis can enhance plant biomass, seed weight, and yield. Taking these data together, we identify a novel positive regulator of auxin response and transport in a crop plant and demonstrate its role in regulating grain size, thus illuminating a new strategy to improve plant productivity.Because it is one of the most important staple food crops cultivated worldwide, improvement of grain yield is a major focus of rice-breeding programs (1). Grain size is one of the determining factors of grain yield (2, 3). A number of quantitative trait loci (QTLs) controlling rice grain size have been identified in recent years (4–11). However, functional mechanisms of these genes remain largely unknown. Because QTLs usually have important functions in determining grain size, many of them have been widely selected in breeding processes or existed in modern elite varieties, and a certain QTL could be only applicable in certain varieties (12). Thus, exploration of new grain size-associated genes and elucidation of their functional mechanisms have great significance for further improvement of rice yield (12).Seed size, as well as other organ size, is controlled by various plant hormones, such as auxin, brassinosteroid, and cytokinin (10, 13, 14). A number of studies have demonstrated that auxin plays a vital role in organ size determination by affecting cell division, cell expansion, and differentiation (15–17). Auxin exists predominantly as indole-3-acetic acid (IAA) in plants, and genetic studies of its biosynthetic genes in Arabidopsis have demonstrated that IAA regulates many aspects of plant growth and development, including stem elongation, lateral branching, vascular development, and tropic growth responses (18, 19). Combined with biochemical studies, the tryptophan (Trp)-dependent IAA biosynthesis pathway has been clearly established involving the YUCCA family flavin monooxgenases (20). Importantly, the two-step pathway is highly conserved throughout the plant kingdom (21). Until very recently, the Trp-independent auxin biosynthetic pathway was elucidated as contributing to early embryogenesis in Arabidopsis (22). Primary auxin signaling is a rapid process initiated from the hormone perception by receptor TIR1, an F-box protein, followed by degradation of the negative regulator AUX/IAA proteins, and further release the downstream auxin response factors (ARFs) (23–26). However, how the ARFs work in plants remains elusive. Auxin transport, generally referring to the cell-to-cell transportation of the hormone directed basipetally from shoots to roots in vascular tissues, plays a critical role in auxin response (18). The transport involves a number of membrane-associated proteins, such as PINs (protein inhibitor of nNOS), AUX1 (AUXIN TRANSPORTER PROTEIN 1), and ABCBs (ATP-BINDING CASSETTE, SUB-FAMILY B PROTEINS) as efflux or influx carriers (27–30). Disruption of auxin transport induced by either gene mutations or chemical inhibitor treatment will lead to diverse development defects, such as decreased lateral organ initiation and defective tropic growth responses (27, 31–34).In this study, we identify a rice mutant, named big grain1-D (Bg1-D) because it is a dominant mutant having extralarge grain size. BG1 encodes a novel plasma membrane-associated protein, and is specifically induced by auxin treatment. We show that BG1 is a new positive regulator of auxin response involved in auxin transport, and demonstrate that manipulation of BG1 expression can greatly improve grain size and plant productivity.     

Immunogenetic biomarkers in inflammatory bowel diseases: Role of the IBD3 region

Many studies have demonstrated the linkage between the IBD3 region (6p21.1-23), an area which encompasses the famous human leukocyte antigen (HLA) complex, and Crohn’s disease (CD) or ulcerative colitis (UC). IBD3 is the only region that meets genome-wide significance, and provides stronger evidence of the linkage than 16p13.1-16q12.2 (IBD1), the locus that contains the susceptibility gene CARD15. However, despite these findings, IBD3 susceptibility genes remain elusive and unclear due to the strong linkage disequilibrium, extensive polymorphism, and high gene density that characterize this area and also due to varying allele frequencies in populations around the world. This area presents an extremely high abundance of genes, including the classical and non-classical major histocompatibility complex (MHC) class I and II genes, and other genes, namely MHC class III genes tumor necrosis factor (TNF)-α and -β, and Hsp, whose proteins play key functions in immunological processes. To date, it is not clear which genes within the MHC family contribute to the IBD pathogenesis, although certain HLA alleles have been associated with IBD. Recent insights into the biological function of other genes encoded within the IBD3 region, such as the MHC class I chain-related (MIC) genes, have led investigators to a more comprehensive exploration of this region. MHC class I chain-related molecule A (MICA) is highly polymorphic and interacts with NKG2D, its receptor on the surface of NK, Tγδ and T CD8⁺ cells. Increased expression of MICA in intestinal epithelial cells and increased expression of NKG2D in CD4⁺ T cells (lamina propria) in patients with CD have also been reported. MICA alleles have also been associated with IBD, and a variation at amino acid position 129 of the α2-heavy chain domain seems to categorize MICA alleles into strong and weak binders of NKG2D receptor, thereby influencing the effector cells’ function. In this regard, a relevant role of MICA-129-Val/Met single nucleotide polymorphism has recently been implicated in the pathogenesis of IBD. TNF-α and -β also play an important role in inflammatory response. In fact, IBD is commonly treated with TNF-α inhibitors. Additionally, polymorphisms of TNF-α gene are known to affect the gene expression level and particular TNF-α genotypes may influence the response of IBD patients treated with TNF-α inhibitors.     

High prevalence of PfCRT K76T mutation in Plasmodium falciparum isolates in Ghana

Plasmodium falciparum has successfully developed resistance to almost all currently used antimalarials. A single nucleotide polymorphism in the P. falciparum chloroquine resistance transporter (Pfcrt) gene at position 76 resulting in a change in coding from lysine to threonine (K76T) has been implicated to be the corner stone of chloroquine resistance. Widespread resistance to chloroquine in endemic regions led to its replacement with other antimalarials. In some areas this replacement resulted in a reversion of the mutant T76 allele to the wild-type K76 allele. This study was conducted to determine the prevalence of the K76T mutation of the Pfcrt gene eight years after the ban on chloroquine sales and use. A cross-sectional study was conducted in 6 regional hospitals in Ghana. PCR-RFLP was used to analyse samples collected to determine the prevalence of Pfcrt K76T mutation. Of the 1318 participants recruited for this study, 246 were found to harbour the P. falciparum parasites, of which 60.98% (150/246) showed symptoms for malaria. The prevalence of the Pfcrt T76 mutant allele was 58.54% (144/246) and that of the K76 wild-type allele was 41.46% (102/246). No difference of statistical significance was observed in the distribution of the alleles in the symptomatic and asymptomatic participants (P = 0.632). No significant association was, again, observed between the alleles and parasite density (P = 0.314), as well as between the alleles and Hb levels of the participants (P = 0.254). Notwithstanding the decline in the prevalence of the Pfcrt T76 mutation since the antimalarial policy change in 2004, the 58.54% prevalence recorded in this study is considered high after eight years of the abolishment of chloroquine usage in Ghana. This is in contrast to findings from other endemic areas where the mutant allele significantly reduced in the population after a reduction chloroquine use.     

Functional analysis of human mismatch repair gene mutations identifies weak alleles and polymorphisms capable of polygenic interactions

Many of the mutations reported as potentially causing Lynch syndrome are missense mutations in human mismatch repair (MMR) genes. Here, we used a Saccharomyces cerevisiae-based system to study polymorphisms and suspected missense mutations in human MMR genes by modeling them at the appropriate S. cerevisiae chromosomal locus and determining their effect on mutation rates. We identified a number of weak alleles of MMR genes and MMR gene polymorphisms that are capable of interacting with other weak alleles of MMR genes to produce strong polygenic MMR defects. We also identified a number of alleles of MSH2 that act as if they inactivate the Msh2-Msh3 mispair recognition complex thus causing weak MMR defects that interact with an msh6Δ mutation to result in complete MMR defects. These results indicate that weak MMR gene alleles capable of polygenic interactions with other MMR gene alleles may be relatively common.