Polymorphic SNPs Research Articles

A 36 Mb terminal deletion of chromosome 2BL is responsible for a wheat semi-dwarf mutation

Reduced plant height is one of the most important traits related to lodging resistance and crop yield. The use of reduced height genes has been one of the main features in breeding modern high-yielding wheat varieties with less lodging. A spontaneous dwarf mutant DD399 was identified in a high yielding, gibberellic acid (GA)-insensitive, lodging-resistant variety Nongda 399 (ND399). Significant differences in upper internode lengths between mutant DD399 and wild type ND399 were caused by reduced cell elongation. The plant height of ND399 × DD399 F1 hybrids was intermediate between the parents, indicating incomplete dominance or a dose–response effect of a reduced height gene. Plant height showed continuous distribution in the F2 population, and segregation distortion was observed among the 2292 F2:3 progenies. The reduced height mutation was characterized by Illumina 90 K iSelect SNP genotyping and bulked segregant RNA-Seq (BSR-Seq) analysis of the segregating population. A concentrated cluster of polymorphic SNPs associated with the reduced height phenotype was detected in the distal region of chromosome arm 2BL. Co-segregation of reduced height phenotype with the clustered markers revealed a 36 Mb terminal deletion of chromosome 2BL in mutant DD399.

Read_haps: using read haplotypes to detect same species contamination in DNA sequences.

Data analysis is requisite on reliable data. In genetics this includes verifying that the sample is not contaminated with another, a problem ubiquitous in biology. In human, and other diploid species, DNA contamination from the same species can be found by the presence of three haplotypes between polymorphic SNPs. read_haps is a tool that detects sample contamination from short read whole genome sequencing data. github.com/DecodeGenetics/read_haps.

Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes.

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.).

Rye (Secale cereale L.) responds strongly to changes in heterozygosity with hybrids portraying strong heterosis effect on all developmental and yielding characteristics. In order to achieve the highest potential heterosis effect parental lines must originate from genetically distinct gene pools. Here we report the first comprehensive SNP-based population study of an elite germplasm using fertilization control system for hybrid breeding in rye that is genetically different to the predominating P-type. In total 376 inbred lines from Nordic Seed Germany GmbH were genotyped for 4419 polymorphic SNPs. The aim of this study was to confirm and quantify the genetic separation of parental populations, unveil their genetic characteristics and investigate underlying population structures. Through a palette of complimenting analysis, we confirmed a strong genetic differentiation (FST = 0.332) of parental populations validating the germplasms suitability for hybrid breeding. These were, furthermore, found to diverge considerably in several features with the maternal population portraying a strong population structure characterized by a narrow genetic profile, small effective population size and high genome-wise linkage disequilibrium. We propose that the employed male-sterility system putatively constitutes a population determining parameter by influencing the rate of introducing novel genetic variation to the parental populations. Functional analysis of linkage blocks led to identification of a conserved segment on the distal 4RL chromosomal region annotated to the Rfp3 male-fertility restoration 'Pampa' type gene. Findings of our study emphasized the immediate value of comprehensive population studies on elite breeding germplasms as a pre-requisite for application of genomic-based breeding techniques, introgression of novel material and to support breeder decision-making.

KASP™ based markers reveal a population sub-structure in temperate rice (Oryza sativa L.) germplasm and local landraces grown in the Kashmir valley, north-western Himalayas

The conservation and utilization of germplasm is contingent on its proper characterization at morphological or molecular levels. The present study aimed to elucidate the population sub-structure of 470 temperate rice germplasm collections of the Kashmir Valley. Analysis was carried out using KASP (Kompetitive Allele Specific PCR) assay on 213 genomic loci. Of these, a restricted set of 114 KASP loci were selected by the elimination of redundant, i.e. tightly linked markers based on map positions. STRUCTURE grouping was carried out to reveal three distinct sub-populations, K1, K2 and K3 comprising of 209, 156 and 105 germplasm accessions, respectively. Population FST values for K1, K2 and K3 were at 0.60, 0.24, 0.69, respectively, with highest pair-wise FST obtained between K2 and K3 (0.53). Analysis using the restricted set of 114 markers gave a better inferred membership with a low average admixture of 15.1% compared with 22.6% based on the whole marker set. An improved agreement between STRUCTURE grouping and principal coordinate analysis was reached using the restricted marker set. ΦST values calculated based on nucleotide diversity also suggested three sub-populations: K2, mostly indica germplasm; K1 mostly exotic temperate japonica; and K3, local japonica varieties and landraces. Polymorphic SNPs and haplotypes were discovered which discriminated the three sub-populations. Fifteen KASP markers were most important in discriminating K2 from K1 and K3 and included SNPs associated with domestication within the Wx, Ghd7 and Ghd8 genes. KASP markers are cheaper than SSR markers. Some of the KASP markers were highly discriminatory, using both model and distance based approaches, and so can be used as a cost-effective tool for efficient maintenance and use of rice genetic resources.

Polymorphism of candidate genes associated with reproductive performance in crossbred pigs

This investigation was done to analyze the polymorphism of 5 SNPs in candidate genes associated with reproductive performance in crossbred pig population by PCR-RFLP. The results revealed that out of 5 SNPs genotyped, 2 were polymorphic and 3 were monomorphic. Genotypic frequency of crossbred pigs were CC (100%) for ESR1; GG (21%), GT 65%) and TT (14%) for Prei3; CC (100%) for FSHβ; AA (100%) for OPN and CC (21%), CT (63%) and TT (16%) for CDK20 SNPs, respectively. Allelic frequencies for these SNPs {ESR1 (c.1227C>T), Prei3 (T802G), FSHβ (c.930A>G), OPN (c.425G>A) and CDK20 (T96C)} were 1.00 (C), 0.53 and 0.47 (G/T), 1.00 (C), 1.00 (A) and 0.52 and 0.48 (C/T), respectively. The least squares analysis revealed that both polymorphic SNPs had non-significant effect on litter traits. The values of PIC, heterozygosity and allelic diversity indicated that crossbred population under investigation was of intermediate diversity for both polymorphic SNP loci.

Identification and genetic analysis of EMS-mutagenized wheat mutants conferring lesion-mimic premature aging

BackgroundLesion-mimic and premature aging (lmpa) mutant lmpa1 was identified from the ethyl methane sulfonate (EMS) mutant library in the bread wheat variety Keda 527 (KD527) background. To reveal the genetic basis of lmpa1 mutant, phenotypic observations and analyses of chlorophyll content and photosynthesis were carried out in lmpa1, KD527 and their F1 and F2 derivatives. Further, bulked segregation analysis (BSA) in combination with a 660 K SNP array were conducted on the F2 segregation population of lmpa1/Chinese spring (CS) to locate the lmpa1 gene.ResultsMost agronomic traits of lmpa1 were similar to those of KD527 before lesion-like spots appeared. Genetic analysis indicated that the F1 plants from the crossing of lmpa1 and KD527 exhibited the lmpa phenotype and the F2 progenies showed a segregation of normal (wild type, WT) and lmpa, with the ratios of lmpa: WT = 124:36(χ2 = 1.008 < =3.841), indicating that lmpa is a dominant mutation. The combination of BSA and the SNP array analysis of CS, lmpa1 and lmpa1/CS F2 WT pool (50 plants) and lmpa pool (50 plants) showed that polymorphic SNPs were enriched on chromosome 5A, within a region of 30–40 Mb, indicating that the wheat premature aging gene Lmpa1 was probably located on the short arm of chromosome 5A.ConclusionsEMS-mutagenized mutant lmpa1 deriving from elite wheat line KD527 conferred lmpa. Lmpa phenotype of lmpa1 mutant is controlled by a single dominant allele designated as Lmpa1, which affected wheat growth and development and reduced the thousand grain weight (tgw) of single plant in wheat. The gene Lmpa1 was tentatively located within the region of 30–40 Mb near to the short arm of chromosome 5A.

Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs

BackgroundThe development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq).ResultsBased on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches.ConclusionImportantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.

High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover.

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.

Mapping and candidate gene screening of Cladosporium fulvum resistance gene Cf‐12 in tomato (Solanum lycopersicum) by high‐throughput sequencing

AbstractTomato leaf mould disease is a serious foliar disease caused by Cladosporium fulvum, resulting in a significant reduction in yield and quality, especially under protected cultivation. Finding new resistant genes against leaf mould has become one of the important goals of tomato breeding. Cf‐12‐tomato showed good resistance to several C. fulvum races. The Cf‐12 was mapped using re‐sequencing and BSA methods. Allelism test for Cf‐12, Cf‐5 and Cf‐9 was performed. The results showed that Cf‐12 is an independently assigned C. fulvum resistance gene. About 67,853 high‐quality polymorphic SNPs were found and 233 genes were annotated in three associated regions of 5.85 Mb on Chr. 6s. Three genes with typical Cf‐type characters encoding the leucine‐rich repeat receptor‐like protein were screened out. Using qRT‐PCR, structural and phylogenetic analysis, only the Solyc06g008265.1.1‐CGN7495 was finally identified. An effective InDel marker, InD‐3F/1R, was designed for MAS breeding. Our research provides new insights into the mapping of the Cf‐12, and provides a basis for Cf‐12 cloning and the Cf genetic evolution analysis.

Prevalence of polymorphisms in N-acetyltransferase 2 gene among patients of Yakut ethnicity newly diagnosed with pulmonary tuberculosis

Background. Tuberculosis therapy can lead to considerably dissimilar outcomes among individual patients. Some patients benefit from anti-tuberculosis chemotherapy leading to a desired therapeutic effect, while other patients show insufficient or absent response, or develop adverse side effects. Individual response to isoniazid is affected by mutations in the gene encoding N-acetyltransferase 2 (NAT2). Wide variations were observed in distributions of polymorphic NAT2 alleles in human populations depending on race, ethnicity, or geographical origin. No data are available to date on prevalence of NAT2 gene polymorphic variants and acetylation types in Yakut (Sakha) patients with newly diagnosed pulmonary tuberculosis.&#x0D; Aims: the frequencies of NAT2 polymorphic SNPs as well isoniazid acetylation phenotypes were evaluated in the patients cohort of Yakut ethnicity with newly diagnosed pulmonary tuberculosis (PTB). The comparison with, other ethnic groups of Asian origin was done.&#x0D; Methods. Cross-sectional study was conducted among Yakut patient cohorts with newly identified pulmonary tuberculosis. Using real-time PCR the following SNPs were explored: NAT2*5 (rs1801280, Т341С), NAT2*6 (rs1799930, G590A), NAT2*7 (rs1799931, G857A), NAT2*11 (rs1799929, C481T), NAT2*12 (rs1208, A803G), NAT2*13 (rs1041983, C282T). Genetically determined metabolic rates were calculated using NATpred online tool.&#x0D; Results. NAT2 SNPs were assessed, namely *5, *6, *7, *11, *12, and *13. The most frequent in Yakut patients were NAT2*6 and NAT2*13 SNPs (40.9% and 64.4%, respectively). Significant differences were detected in frequencies of NAT2 *5, *11, *12 polymorphisms; all studied NAT2 gene polymorphisms showed meaningful differences in genotype and minor allele prevalence rates after comparison between Yakut population and other Mongoloid ethnic groups (populations of China, Japan, Vietnam). High prevalence of intermediate acetylation type among ethnic Yakuts (58.3%) was established.&#x0D; Conclusions. Certain distinct differences in allelic variants of NAT2 gene and acetylation type prevalence in patients of Yakut ethnic origin newly diagnosed with pulmonary tuberculosis let conclude that the existing genotyping and phenotyping data from studies among other Mongoloid populations cannot be implicitly extrapolated on Yakut people. Pharmacogenetic data on individual response to drugs in Yakut patients should be made use of in clinical practice, to develop personalized isoniazid administration algorithms, with a final goal to make treatment more effective and safe.

The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies

Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet cherry, the fruticosa subgenome of sour cherry, and cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and the avium and the fruticosa subgenomes of sour cherry, respectively. For sweet cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in cherry.

Whole-genome association studies of distribution of developmental abnormalities and other breeding-valuable qualitative traits in offspring of the Russian large-white boars

Выявление областей генома, прямо или опосредованно связанных с признаками пороков развития у домашних свиней, может способствовать идентификации генетических мишеней, используемых в качестве биомаркеров индивидуальных особенностей формирования экстерьера, их метаболического статуса, а также подверженности генетическим заболеваниям. Такие исследования напрямую связаны с повышением экономической эффективности, поскольку позволяют выявлять и исключать из селекционного процесса животных-носителей нежелательных генов, фенотип которых может не проявляться. В данной работе проведен поиск подобных целевых генов и геномных регионов с помощью полногеномных ассоциативных исследований (GWAS) с использованием ДНК-чипов PorcineSNP60K BeadChips (Illumina, San Diego, USA). Проанализировано 48 хряков свиней крупной белой породы селекционно-гибридного центра «Знаменский» Орловской области по 21 недостатку экстерьера и дефектам развития у 39 153 их потомков. Расчеты производили по линейной модели смешанного типа в программном пакете GEMMA. Из изначального сета в 61 000 SNP были отобраны 36 704 полиморфных SNP, в которых найдены 24 полиморфизма, входящих в 11 генов (P < 0.1), статистически значимо коррелирующих с признаками аномалий развития в геноме свиней, такими как атрезия анального отверстия (ARMC7, FANCC, RND3, ENSSSCG00000017216), проблемы с конечностями (PAWR, NTM, OPCML, ENSSSCG00000040250, ENSSSCG00000017018) и тремор поросят (RIC3, ENSSSCG00000032665). Также была выявлена коэкспрессия генов NTM, OPCML и RND3, участвующих в регуляции клеточной адгезии. Проведенная работа подтвердила актуальность применения подобного подхода в полногеномно-ассоциативных исследованиях для детектирования единичных SNP, связанных с отдельными признаками, даже для небольших выборок.

English

Wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Powdery mildew (Pm), caused by Blumeria graminis f. sp. tritici is a severe disease in wheat production. Gene Pm5e, from a Chinese wheat cultivar Fuzhuang 30 has proven to be a valuable resistance source for Pm in breeding. To further map this gene and develop Kompetitive allele-specific PCR (KASP) assays for marker-assisted selection (MAS), a F2 population containing 395 individuals was first phenotyped for Pm resistance, a bulked segregant analysis (BSA) was used to identify polymorphic SNPs using the 35K wheat SNPs chip. 27 polymorphic SNPs between bulks in the Pm5e region were identified and were converted into KASP assays to map Pm5e. A genetic linkage map of Pm5e was constructed with 2 SNP and 2 SSR molecular markers. Pm5e was mapped to a 9.5 cM interval and the two SNP markers AX-95000860 and AX-94638908 were the two closet flanking markers, which delimited Pm5e into a 14 Mb region. Identification of the molecular markers and development of the two KASP assays laid a solid base for MAS of gene Pm5e in breeding. Key words: Linkage map, marker assisted selection, SNP marker, wheat

Ichthyosis with confetti caused by new and recurrent mutations in KRT10 associated with varying degrees of keratin 10 mis-localization

BackgroundIchthyosis with confetti (IWC) is an extremely rare autosomal-dominant genodermatosis characterized by erythroderma with numerous confetti-like pale spots. IWC is caused by mutations in KRT10 (IWC-I) or KRT1 (IWC-II) which affect their tail domains. In IWC-I, the mutations lead to replacement of glycine/serine-rich keratin 10 (K10) tail with arginine- or alanine-rich frameshift motifs, causing K10 mis-localization which might trigger loss of the mutant KRT10 allele via mitotic recombination, leading to genetic reversion. ObjectiveTo investigate mutations in five IWC-I patients and their functional consequences. MethodsWe performed Sanger sequencing of KRT1 and KRT10 in peripheral blood samples of five patients, with highly polymorphic KRT10 SNPs genotyped to confirm loss-of-heterozygosity in the epidermis of pale spots. K10 expression pattern was examined in both patient skin biopsies and HaCaT cells overexpressing mutant KRT10-enhanced green fluorescence protein fusion. ResultsFour novel and one recurrent KRT10 mutations were identified in patient peripheral blood samples but not in the corresponding pale spot epidermis. Two of the mutations, c.1696_1699dupCACA and c.1676dupG, affected residues close to K10 carboxyl terminus and encoded only 3 and 6 arginine residues, which were far fewer than reported previously. Interestingly, imaging analyses for K10 in HaCaT cells overexpressing either of these two mutations and in the corresponding patients' affected skin, showed a remarkably lower level of K10 mis-localization compared to that of other mutations reported in this study. ConclusionsOur findings suggest that the number of arginine residues in the mutant tail may correlate with the level of K10 mis-localization in IWC-I keratinocytes. These results expand the genotypic and phenotypic spectrum of IWC-I.

Evolutionary relevance of lineages in the European black pine (Pinus nigra) in the transcriptomic era

European black pine (Pinus nigra J.F.Arnold) is an ecologically and economically important conifer growing across southern Europe and the Mediterranean Basin in a variety of habitats. Its morphological and ecological variabilities as well as geographic origin are the basis for subspecies level taxonomic identification and forestry practice recommendations. Yet, no true consensus exists and genomic resources are lacking for resolving the taxonomy of P. nigra and assessing its adaptive potential. To provide genetic tools for further research, we generated novel genomic resources using six de novo transcriptomic assemblies representing major biogeographic regions where the species is growing naturally. Using two closely related species, Pinus sylvestris and Pinus halepensis, as outgroups, we identified a set of 2200 nuclear, putatively orthologous, single-copy genes. In addition, we identified a set of 405,624 polymorphic SNPs for P. nigra. Based on these resources, we were able to confirm the division of P. nigra into two wide geographical population groups and to provide new insights into evolutionary dynamics of the species.

Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum)

BackgroundEthiopia has been considered as a center of diversity and the second possible center of domestication of durum wheat. Genetic diversity and population structure analysis in the existing Ethiopian durum wheat germplasm have enormous importance in enhancing breeding effort and for sustainable conservation. Hence, 192 Ethiopian durum wheat accessions comprising 167 landraces collected from major wheat-growing areas of the country and 25 improved varieties released from Debre Zeit and Sinana Agricultural Research Centers, Ethiopia in different years (1994–2010) were assembled for the current study.ResultsThe panel was genotyped with a High-density 90 K wheat SNP array by Illumina and generated 15,338 polymorphic SNPs that were used to analyze the genetic diversity and to estimate the population structure. Varied values of genetic diversity indices were scored across chromosomes and genomes. Genome-wide mean values of Nei’s gene diversity (0.246) and polymorphism information content (0.203) were recorded signifying the presence of high genetic diversity within this collection. Minor allele frequency of the genome varied with a range of 0.005 to 0.5 scoring a mean value of 0.175. Improved varieties clustered separately to landraces in population structure analysis resulted from STRUCTURE, PCA and neighbor joining tree. Landraces clustering was irrespective of their geographical origin signifying the presence of higher admixture that could arise due to the existence of historical exchanges of seeds through informal seed system involving regional and countrywide farming communities in Ethiopia.ConclusionsSustainable utilization and conservation of this rich Ethiopian durum wheat genetic resource is an irreplaceable means to cope up from the recurrent climate changes and biotic stresses happening widely and thereby able to keep meeting the demand of durum productivity for the ever-growing human population.

In Silico Identification of QTL-Based Polymorphic Genes as Salt-Responsive Potential Candidates through Mapping with Two Reference Genomes in Rice.

Recent advances in next generation sequencing have created opportunities to directly identify genetic loci and candidate genes for abiotic stress responses in plants. With the objective of identifying candidate genes within the previously identified QTL-hotspots, the whole genomes of two divergent cultivars for salt responses, namely At 354 and Bg 352, were re-sequenced using Illumina Hiseq 2500 100PE platform and mapped to Nipponbare and R498 genomes. The sequencing results revealed approximately 2.4 million SNPs and 0.2 million InDels with reference to Nipponbare while 1.3 million and 0.07 million with reference to R498 in two parents. In total, 32,914 genes were reported across all rice chromosomes of this study. Gene mining within QTL hotspots revealed 1236 genes, out of which 106 genes were related to abiotic stress. In addition, 27 abiotic stress-related genes were identified in non-QTL regions. Altogether, 32 genes were identified as potential genes containing polymorphic non-synonymous SNPs or InDels between two parents. Out of 10 genes detected with InDels, tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200 were found in the known salinity tolerant donor varieties. Our findings on different haplotypes would be useful in developing resilient rice varieties for abiotic stress by haplotype-based breeding studies.

QTL Mapping of Kernel Traits and Validation of a Major QTL for Kernel Length-Width Ratio Using SNP and Bulked Segregant Analysis in Wheat

One RIL population derived from the cross between Dalibao and BYL8 was used to examine the phenotypes of kernel-related traits in four different environments. Six important kernel traits, kernel length (KL), kernel width (KW), kernel perimeter (KP), kernel area (KA), kernel length/width ratio (KLW), and thousand-kernel weight (TKW) were evaluated in Yangling, Shaanxi Province, China (2016 and 2017), Nanyang, Henan Province, China (2017) and Suqian, Jiangsu Province, China (2017). A genetic linkage map was constructed using 205 SSR markers, and a total of 21 significant QTLs for KL, KW, KP, KA, KLW and TKW were located on 10 of the 21 wheat chromosomes, including 1A, 1B, 2A, 2B, 2D, 3D, 4D, 5A, 5B, and 7D, with a single QTL in different environments explaining 3.495–30.130% of the phenotypic variation. There were four loci for KLW, five for KA, five for KL, three for KP, two for KW, and two for TKW among the detected QTLs. We used BSA + 660 K gene chip technology to reveal the positions of major novel QTLs for KLW. A total of 670 out of 5285 polymorphic SNPs were detected on chromosome 2A. The SNPs in 2A are most likely related to the major QTL, and there may be minor QTLs on 5B, 7A, 3A and 4B. SSR markers were developed to verify the chromosome region associated with KLW. A linkage map was constructed with 7 SSR markers, and a major effect QTL was identified within a 21.55 cM interval, corresponding to a physical interval of 10.8 Mb in the Chinese Spring RefSeq v1.0 sequence. This study can provide useful information for subsequent construction of fine mapping and marker-assisted selection breeding.

Genomic prediction of grain yield in contrasting environments for white lupin genetic resources

Germplasm collections hold several thousands of white lupin (Lupinus albus L.) accessions. Genome-enabled models with good predictive ability for specific environments could provide a cost-efficient means to identify promising genetic resources for breeding programmes. This study provided an unprecedented assessment of genome-enabled predictions for white lupin grain yield, focusing on (i) a world collection of 109 landraces and 8 varieties phenotyped in three European sites with contrasting climate (Mediterranean, subcontinental or oceanic) and sowing time (data set 1); (ii) 78 geographically diversified landrace genotypes and three variety genotypes phenotyped in moisture-favourable and severely drought-prone managed environments (data set 2). The interest of predictions for individual genotypes was justified by large within-landrace variation for yield responses. Ridge regression BLUP (rrBLUP) and Bayesian Lasso (BL) models exploited allele frequencies (estimated from 3 to 4 genotypes per landrace) of 10,782 polymorphic SNPs for data set 1, and allele values of 9937 polymorphic SNPs for data set 2, following ApeKI-based genotyping-by-sequencing characterization. Compared with BL, rrBLUP displayed similar predictive ability for data set 1 and better predictive ability for data set 2. Best-predictive models displayed intra-environment predictive ability for the five test environments in the range 0.47–0.76. Cross-environment predictions between pairs of environments with positive genetic correlation, i.e., autumn-sown subcontinental vs Mediterranean sites, and moisture-favourable vs drought-prone environments, exhibited a predictive ability range of 0.40–0.51 and a predictive accuracy range of 0.48–0.61. Our results support the exploitation of genomic predictions and provide economic justification for the genotyping of germplasm collections of white lupin.