Yield-related Quantitative Trait Loci Research Articles

Integrative multi-omics analysis reveals genetic and heterotic contributions to male fertility and yield in potato.

The genetic analysis of potato is hampered by the complexity of tetrasomic inheritance. An ongoing effort aims to transform the clonally propagated tetraploid potato into a seed-propagated diploid crop, which would make genetic analyses much easier owing to disomic inheritance. Here, we construct and report the large-scale genetic and heterotic characteristics of a diploid F2 potato population derived from the cross of two highly homozygous inbred lines. We investigate 20,382 traits generated from multi-omics dataset and identify 25,770 quantitative trait loci (QTLs). Coupled with gene expression data, we construct a systems-genetics network for gene discovery in potatoes. Importantly, we explore the genetic basis of heterosis in this population, especially for yield and male fertility heterosis. We find that positive heterotic effects of yield-related QTLs and negative heterotic effects of metabolite QTLs (mQTLs) contribute to yield heterosis. Additionally, we identify a PME gene with a dominance heterotic effect that plays an important role in male fertility heterosis. This study provides genetic resources for the potato community and will facilitate the application of heterosis in diploid potato breeding.

Pleiotropic Quantitative Trait Loci (QTL) Mining for Regulating Wheat Processing Quality- and Yield-Related Traits.

To investigate the genetic basis of processing quality- and yield-related traits in bread wheat (Triticum aestivum L., AABBDD), a systematic analysis of wheat processing quality- and yield-related traits based on genome-wide association studies (GWASs) of 285 regional test lines of wheat from Hebei province, China, was conducted. A total of 87 quantitative trait loci (QTL), including twenty-one for water absorption (WA), four for wet gluten content, eight for grain protein content, seventeen for dough stability time (DST), thirteen for extension area (EA), twelve for maximum resistance (MR), five for thousand-grain weight (TGW), one for grain length, and six for grain width were identified. These QTL harbored 188 significant single-nucleotide polymorphisms (SNPs). Twenty-five SNPs were simultaneously associated with multiple traits. Notably, the SNP AX-111015470 on chromosome 1A was associated with DST, EA, and MR. SNPs AX-111917292 and AX-109124553 on chromosome 5D were associated with wheat WA and TGW. Most processing quality-related QTL and seven grain yield-related QTL identified in this study were newly discovered. Among the surveyed accessions, 18 rare superior alleles were identified. This study identified significant QTL associated with quality-related and yield-related traits in wheat, and some of them showed pleiotropic effects. This study will facilitate molecular designs that seek to achieve synergistic improvements of wheat quality and yield.

Yield-related quantitative trait loci identification and lint percentage hereditary dissection under salt stress in upland cotton.

Salinity is frequently mentioned as a major constraint in worldwide agricultural production. Lint percentage (LP) is a crucial yield-component in cotton lint production. While the genetic factors affect cotton yield in saline soils are still unclear. Here, we employed a recombinant inbred line population in upland cotton (Gossypium hirsutum L.) and investigated the effects of salt stress on five yield and yield component traits, including seed cotton yield per plant, lint yield per plant, boll number per plant, boll weight, and LP. Between three datasets of salt stress (E1), normal growth (E2), and the difference values dataset of salt stress and normal conditions (D-value), 87, 82, and 55 quantitative trait loci (QTL) were detectable, respectively. In total, five QTL (qLY-Chr6-2, qBNP-Chr4-1, qBNP-Chr12-1, qBNP-Chr15-5, qLP-Chr19-2) detected in both in E1 and D-value were salt related QTL, and three stable QTL (qLP-Chr5-3, qLP-Chr13-1, qBW-Chr5-5) were detected both in E1 and E2 across 3 years. Silencing of nine genes within a stable QTL (qLP-Chr5-3) highly expressed in fiber developmental stages increased LP and decreased fiber length (FL), indicating that multiple minor-effect genes clustered on Chromosome 5 regulate LP and FL. Additionally, the difference in LP caused by Gh_A05G3226 is mainly in transcription level rather than in the sequence difference. Moreover, silencing of salt related gene (GhDAAT) within qBNP-Chr4-1 decreased salt tolerance in cotton. Our findings shed light on the regulatory mechanisms underlining cotton salt tolerance and fiber initiation.

Genome-wide association study revealed the reason for the decrease in grain iron concentration during wheat breeding process in China

Iron (Fe) deficiency affects over two billion people worldwide. Developing high-yielding wheat (Triticum aestivum L.) cultivars with high grain Fe concentration (GFeC) is a key step toward alleviating malnutrition in humans. In this study, we used a diversity panel of 388 wheat accessions to examine the GFeC in four field environments. We found that the mean GFeC of the four environments decreased with the release year. And GFeC showed poor correlation with grain yield or the three yield factors in the four environments. Importantly, wheat cultivars in the major wheat-producing region of China showed the lowest GFeC. The GFeC phenotype was used for a genome-wide association study (GWAS) using a 660 K single-nucleotide polymorphism (SNP) chip, and 17 quantitative trait loci (QTLs) were identified on chromosomes 3B, 4 A, 5 A, 6B, 6D, 7 A, 7B, and 7D. However, no universal QTLs were detected among the 17 identified QTLs and 2280 yield-related QTLs. Through allelic analysis, two homologous genes, TraesCS7A01G197400 and TraesCS7D01G198900, were identified as potential candidate genes for GFeC, while the favourable alleles for GFeC were lost during the selection breeding process in China. The insights gained from this study showed that the yield dilution effect was not applied to the decrease in GFeC, which should be mainly caused by the loss of favourable alleles during the wheat breeding process in China. Therefore, wheat breeders should pay more attention to other traits to improve GFeC rather than the yield dilution effect.

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones.

Heat stress during the potato growing season reduces tuber marketable yield and quality. Tuber quality deterioration includes external (heat sprouts, chained tubers, knobs) and internal (vascular discoloration, hollow heart, internal heat necrosis) tuber defects, as well as a reduction in their specific gravity and increases in reducing sugars that result in suboptimal (darker) processed products (french fries and chips). Successfully cultivating potatoes under heat-stress conditions requires planting heat-tolerant varieties that can produce high yields of marketable tubers, few external and internal tuber defects, high specific gravity, and low reducing sugars (in the case of processing potatoes). Heat tolerance is a complex trait, and understanding its genetic basis will aid in developing heat-tolerant potato varieties. A panel of 217 diverse potato clones was evaluated for yield and quality attributes in Dalhart (2019 and 2020) and Springlake (2020 and 2021), Texas, and genotyped with the Infinium 22 K V3 Potato Array. A genome-wide association study was performed to identify genomic regions associated with heat-tolerance traits using the GWASpoly package. Quantitative trait loci were identified on chromosomes 1, 3, 4, 6, 8, and 11 for external defects and on chromosomes 1, 2, 3, 10, and 11 for internal defects. Yield-related quantitative trait loci were detected on chromosomes 1, 6, and 10 pertaining to the average tuber weight and tuber number per plant. Genomic-estimated breeding values were calculated using the StageWise package. Clones with low genomic-estimated breeding values for tuber defects were identified as donors of good traits to improve heat tolerance. The identified genomic regions associated with heat-tolerance attributes and the genomic-estimated breeding values will be helpful to develop new potato cultivars with enhanced heat tolerance in potatoes.

Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci.

Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis. A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B). A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1-25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).

KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)

Super Basmati is an elite variety with extra-long grains and superior quality but its yield is severely affected by water stress. Recombinant inbred lines (RILs) developed from the cross of Super Basmati and IR55419-04 (a coarse grained variety with high yield potential) were used to identify and map yield-related quantitative trait loci (QTLs) under normal field conditions. Genotypes for 244 KASP markers were obtained from 188 F9 RILs and a linkage map constructed of 1369.4 cM, with average marker interval of 10.5 cM. Eleven agronomic traits were phenotyped in RILs and parents. Composite interval mapping and inclusive composite interval mapping model identified 21 common QTLs related to nine agronomic traits; of the QTLs identified, twelve mapped at novel positions. LOD scores ranged from 2.51 for number of filled grains (qFG1.1) to 16.8 for plant height (qPH1.1). Four major effect QTLs could explain 20% of variation related for plant height, hundred-grain weight and grain width. Alleles from IR55419-04 improved grain filling, grain weight and grain width, while alleles from Super Basmati contributed to longer grains, panicles and flag leaves. Putative candidate genes were identified for 18 yield-related QTLs. These results validate the use of KASP genotyping for QTL mapping of yield-related traits in a bi-parental segregating population. SNPs in the QTLs identified in this study can be used in marker assisted selection for yield components to improve Basmati rice.

Introgression of QTL from Aegilops tauschii enhances yield-related traits in common wheat

To break the narrow diversity bottleneck of the wheat D genome, a set of Aegilops tauschii-wheat introgression (A-WI) lines was developed by crossing Ae. tauschii accession T015 with common wheat elite cultivar Zhoumai 18 (Zhou18). A high-density genetic map was constructed based on Single Nucleotide Polymorphism (SNP) markers and 15 yield-related traits were evaluated in 11 environments for detecting quantitative trait loci (QTL). A total of 27 environmentally stable QTL were identified in at least five environments, 20 of which were derived from Ae. tauschii T015, explaining up to 24.27% of the phenotypic variations. The major QTL for kernel length (KL), QKl-2D.5, was delimited to a physical interval of approximately 2.6 Mb harboring 52 candidate genes. Three Kompetitive Allele Specific PCR (KASP) markers were successfully developed based on nonsynonymous nucleotide mutations of candidate gene AetT093_2Dv1G100900.1 and showed that A-WI lines with the T015 haplotype had significantly longer KL than the Zhou18 haplotype across all 11 environments. Four primary valuable A-WIs with good trait performance and carrying yield-related QTL were selected for breeding improvement. The results will facilitate the efficient transfer of beneficial genes from Ae. tauschii into wheat cultivars to improve wheat yield and other traits.

Fine mapping of a major QTL qHYF_B06 for peanut yield

High yield is a major objective for peanut (Arachis hypogaea L.) breeding worldwide. However, fewer yield-related quantitative trait loci (QTL) have been reported in peanut than in other staple food crops such as rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). This study aimed to identify stable major-effect QTL associated with pod yield per plant, hundred-pod weight for double-seeded pods, hundred-seed weight, shelling percentage, and pod number per plant, allowing us to predict candidate genes by means of transcriptome and genome sequencing. To this end, we used a population of recombinant inbred lines comprising 192 F9:11 families derived from a JH6 × KX01-6 cross to construct a high-resolution genetic map (1705.7 cM) consisting of 2273 polymorphic SNPs, with 0.75 cM (on average) between adjacent SNPs. We identified two high-confidence, yield-related QTL, qHYF_A08 and qHYF_B06, explaining 5.78%–31.40% of phenotypic variation and with LOD values of 5.10–24.48, in six environments. qHYF_A08 mainly explained the variation in shelling percentage, whereas qHYF_B06 explained variation in hundred-pod weight and hundred-seed weight and accounted for 8.77%–31.40% of the variation in effective pod number per plant, pod number per plant, and shelling percentage. We narrowed down qHYF_B06 to an 890-kb interval using an advanced mapping population. Transcriptome and genome analyses revealed that only Arahy.129FS0 and Arahy.3R9A5K in the candidate mapping interval were differentially expressed between JH6 and KX01-6, with substantial structural variations in their promoter and coding regions. Genotypes of 208 peanut accessions determined using a diagnostic CAPS marker suggested that the two haplotypes of Arahy.3R9A5K were highly associated with hundred-seed weight and hundred-pod weight; this diagnostic CAPs marker could therefore be useful for selecting high-yielding lines during peanut breeding. Overall, our results provide valuable information for cloning alleles with favorable effects on peanut yield.

Discovery of common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits in Brassica napus L.

Common loci and candidate genes for controlling salt-alkali tolerance and yield-related traits were identified in Brassica napus combining QTL mapping with transcriptome under salt and alkaline stresses. The yield of rapeseed (Brassica napus L.) is determined by multiple yield-related traits, which are susceptible to environmental factors. Many yield-related quantitative trait loci (QTLs) have been reported in Brassica napus; however, no studies have been conducted to investigate both salt-alkali tolerance and yield-related traits simultaneously. Here, specific-locus amplified fragment sequencing (SLAF-seq) technologies were utilized to map the QTLs for salt-alkali tolerance and yield-related traits. A total of 65 QTLs were identified, including 30 QTLs for salt-alkali tolerance traits and 35 QTLs for yield-related traits, accounting for 7.61-27.84% of the total phenotypic variations. Among these QTLs, 18 unique QTLs controlling two to four traits were identified by meta-analysis. Six novel and unique QTLs were detected for salt-alkali tolerance traits. By comparing these unique QTLs for salt-alkali tolerance traits with those previously reported QTLs for yield-related traits, seven co-localized chromosomal regions were identified on A09 and A10. Combining QTL mapping with transcriptome of two parents under salt and alkaline stresses, thirteen genes were identified as the candidates controlling both salt-alkali tolerance and yield. These findings provide useful information for future breeding of high-yield cultivars resistant to alkaline and salt stresses.

Dissecting the key genomic regions underlying high yield potential in common wheat variety ‘Kenong 9204’

The foundation parents play key roles in the genetic improvement of both yield potential and end-use quality in wheat. Characterizing the genetic basis that underlies certain beneficial traits in the foundation parents will provide theoretical reference for molecular breeding by a design approach. ‘Kenong 9204’ (KN9204) is a candidate foundation parent characterized by ideotype, high yield potential, and particularly high nitrogen fertilizer utilization. To better understand the genetic basis of its high yield potential, high throughput whole-genome re-sequencing (10×) was performed on KN9204, its parental lines and its derivatives. A high-resolution genetic composition map of KN9204 was constructed, which showed the parental origin of the favorable genomic segments based on the identification of excellent yield-related quantitative trait loci (QTL) from a bi-parental mapping population. Xiaoyan 693 (XY693), a wheat–Thinopyrum ponticum partial amphidiploid, contributed a great deal to the high yield potential of KN9204, and three major stable QTLs from XY693 were fine mapped. The transmissibility of key genomic segments from KN9204 to its derivatives were delineated, indicating that haplotype blocks containing beneficial gene combinations were conserved along with directional selection by breeders. Evidence for selection sweeps in the breeding programs was identified. This study provides a theoretical reference for the breeding of high-yield wheat varieties by a molecular design approach.

Mapping QTLs for Reproductive Stage Salinity Tolerance in Rice Using a Cross between Hasawi and BRRI dhan28.

Salinity stress is a major constraint to rice production in many coastal regions due to saline groundwater and river sources, especially during the dry season in coastal areas when seawater intrudes further inland due to reduced river flows. Since salinity tolerance is a complex trait, breeding efforts can be assisted by mapping quantitative trait loci (QTLs) for complementary salt tolerance mechanisms, which can then be combined to provide higher levels of tolerance. While an abundance of seedling stage salinity tolerance QTLs have been mapped, few studies have investigated reproductive stage tolerance in rice due to the difficulty of achieving reliable stage-specific phenotyping techniques. In the current study, a BC1F2 mapping population consisting of 435 individuals derived from a cross between a salt-tolerant Saudi Arabian variety, Hasawi, and a salt-sensitive Bangladeshi variety, BRRI dhan28, was evaluated for yield components after exposure to EC 10 dS/m salinity stress during the reproductive stage. After selecting tolerant and sensitive progeny, 190 individuals were genotyped by skim sequencing, resulting in 6209 high quality single nucleotide polymorphic (SNP) markers. Subsequently, a total of 40 QTLs were identified, of which 24 were for key traits, including productive tillers, number and percent filled spikelets, and grain yield under stress. Importantly, three yield-related QTLs, one each for productive tillers (qPT3.1), number of filled spikelets (qNFS3.1) and grain yield (qGY3.1) under salinity stress, were mapped at the same position (6.7 Mb or 26.1 cM) on chromosome 3, which had not previously been associated with grain yield under salinity stress. These QTLs can be investigated further to dissect the molecular mechanisms underlying reproductive stage salinity tolerance in rice.

Detection of Stable Elite Haplotypes and Potential Candidate Genes of Boll Weight Across Multiple Environments via GWAS in Upland Cotton.

Boll weight (BW) is a key determinant of yield component traits in cotton, and understanding the genetic mechanism of BW could contribute to the progress of cotton fiber yield. Although many yield-related quantitative trait loci (QTLs) responsible for BW have been determined, knowledge of the genes controlling cotton yield remains limited. Here, association mapping based on 25,169 single-nucleotide polymorphisms (SNPs) and 2,315 insertions/deletions (InDels) was conducted to identify high-quality QTLs responsible for BW in a global collection of 290 diverse accessions, and BW was measured in nine different environments. A total of 19 significant markers were detected, and 225 candidate genes within a 400 kb region (± 200 kb surrounding each locus) were predicted. Of them, two major QTLs with highly phenotypic variation explanation on chromosomes A08 and D13 were identified among multiple environments. Furthermore, we found that two novel candidate genes (Ghir_A08G009110 and Ghir_D13G023010) were associated with BW and that Ghir_D13G023010 was involved in artificial selection during cotton breeding by population genetic analysis. The transcription level analyses showed that these two genes were significantly differentially expressed between high-BW accession and low-BW accession during the ovule development stage. Thus, these results reveal valuable information for clarifying the genetic basics of the control of BW, which are useful for increasing yield by molecular marker-assisted selection (MAS) breeding in cotton.

Identification of Soybean Yield QTL in Irrigated and Rain-Fed Environments

Drought is the primary abiotic stress that limits yield of soybean (Glycine max (L.) Merr.). The study aimed to identify yield-related quantitative trait loci (QTLs) in soybeans using a population of 160 F4-derived lines from ‘Hutcheson’ × PI 471938 crosses, which were cultivated under rain-fed and irrigated conditions. Seed yield was determined based on a total of nine irrigated and five rain-fed environments over two years. Twenty and twenty-seven SSR markers associated with yield (p ≤ 0.05) were identified in the irrigated and rain-fed environments, respectively. Four markers accounted for 22% of the yield variation in the irrigated environments (IR-YLD) and five markers explained 34% of the yield variation in the rain-fed environments (RF-YLD). Two independent IR-YLD and RF-YLD QTLs on chromosome (Chr) 13 (LG-F) were mapped to the Satt395-Sat_074 interval (4.2 cM) and near Sat_375 (3.0 cM), which explained 8% (LOD = 2.6) and 17% (LOD = 5.5) of the yield variation, respectively. The lines homozygous for the Hutcheson allele at the IR-YLD QTL linked to Sat_074 averaged 100 kg ha−1 higher yield than the lines homozygous for the PI 471938 allele. At two independent RF-YLD QTLs on Chr 13 and Chr 17, the lines homozygous for the PI 471938 alleles were 74 to 101 kg ha−1 higher in yield than the lines homozygous for the Hutcheson alleles. Three of the five significant SSR markers associated with RF-YLD were located in a genomic region known for canopy-wilting QTLs, in which the favorable alleles were inherited from PI 471938. The identification of yield-QTLs under the respective rain-fed and irrigated environments provides knowledge regarding differential responses of yield under different irrigation conditions, which will be helpful in developing high-yielding soybean cultivars.

Multi-Locus Genome-Wide Association Study of Four Yield-Related Traits in Chinese Wheat Landraces.

Wheat (Triticum aestivum L.) is one of the most important crops in the world. Here, four yield-related traits, namely, spike length, spikelets number, tillers number, and thousand-kernel weight, were evaluated in 272 Chinese wheat landraces in multiple environments. Five multi-locus genome-wide association studies (FASTmrEMMA, ISIS EN-BLASSO, mrMLM, pKWmEB, and pLARmEB) were performed using 172,711 single-nucleotide polymorphisms (SNPs) to identify yield-related quantitative trait loci (QTL). A total of 27 robust QTL were identified by more than three models. Nine of these QTL were consistent with those in previous studies. The remaining 18 QTL may be novel. We identified a major QTL, QTkw.sicau-4B, with up to 18.78% of phenotypic variation explained. The developed kompetitive allele-specific polymerase chain reaction marker for QTkw.sicau-4B was validated in two recombinant inbred line populations with an average phenotypic difference of 16.07%. After combined homologous function annotation and expression analysis, TraesCS4B01G272300 was the most likely candidate gene for QTkw.sicau-4B. Our findings provide new insights into the genetic basis of yield-related traits and offer valuable QTL to breed wheat cultivars via marker-assisted selection.

Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster.

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar ‘Hwaseong’ and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9OR suggests that the 3 bp insertion was specifically selected in japonica during its domestication. Our findings demonstrate that APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice.

Finding new addictive QTL for yield traits based on a high-density genetic map in hybrid rice

Rice is one of the most important food crops in the world. To discover the genetic basis of yield components in super hybrid rice Nei2You No.6, 386 recombinant inbred sister lines (RISLs) were obtained for mapping quantitative trait loci (QTL) responsible for grain yield per plant, number of panicles per plant, grain number per panicle and 1000-grain weight. Using whole genome re-sequencing, a high-density linkage map consisting of 3203 Bin markers was constructed with total genetic coverage of 1951.1 cM and average density of 0.61 cM. A total of 43 yield-related QTL were mapped to all 12 chromosomes, and each explained 2.40–10.17% phenotypic variance, indicating that the medium and minor effect QTL are genetic basis for high yield of Nei2You No.6. With positive effect, 28 out of the 43 QTL are inherited from the maintainer line (Nei2B). Nine loci, qGYP-6b, qGNP-6c, qNP-7, qTGW-1a, qTGW-5, qTGW-7, qTGW-10b, qTGW-10c and qTGW-12 showed stable effects across multiple environments. Five of these nine QTL were co-located with previously reported QTL, and four novel locus, qNP-7, qGNP-6c, qTGW-7 and qTGW-12, were firstly identified in the present study. Subsequently, qNP-7, qTGW-7 and qTGW-12 were validated using corresponding paired sister lines which differed only in the target genome region. The recombinant inbred sister lines is an effective tool for mapping and confirming QTL of yield-associated traits. Newly detected QTL provide new resource for investigating genetics of yield components and will accelerate molecular breeding in rice.

Construction of a framework linkage map and genetic dissection of drought- and yield-related QTLs in horsegram (Macrotyloma uniflorum)

Horsegram (Macrotyloma uniflorum) is a legume species that is widely distributed throughout the Indian subcontinent. It is considered to be an important dietary protein supplement and nutraceutical. Horsegram has a great potential for fulfilling future pulse crop demand due to its inherent ability to grow under very low moisture conditions. However, the genome structure and organization of this crop is poorly understood, thereby limiting the effective use of gene resources for genetic improvement. We report here our construction of the first framework linkage map of horsegram, consisting of 211 molecular markers (157 SSR, 39 RAPD, 8 ISSR and 7 COS), using a mapping population of 190 recombinant inbred lines derived from a cross between parental lines HPK4 and HPKM249. The map comprises 13 linkage groups (LGs) that span 1423.4 cM, with a mean marker interval of 9.6 cM. Phenotypic data for eight agronomic traits were recorded for 2 years and utilized to detect associated quantitative trait loci (QTLs). Five QTLs for four traits related to drought (days to temporary wilting, root length) and yield (numbers of seeds per plant, days to maturity) were detected on five LGs, with an LOD threshold of 4.0. The linkage and QTL analysis reported here provides useful information for future research work pertaining to the construction of highly enriched genetic maps as well as to the development of drought-resistant and high-yielding varieties of horsegram using marker-assisted selection.

Identification of Yield and Yield-Related Quantitative Trait Loci for the Field High Temperature Condition in Backcross Populations of Rice (Oryza sativaL.)

Identification of Yield and Yield-Related Quantitative Trait Loci for the Field High Temperature Condition in Backcross Populations of Rice (<i>Oryza sativa</i>L.)

Validation of QTLs in Bangladeshi rice landrace Horkuch responsible for salt tolerance in seedling stage and maturation

The upsurge in global temperatures and the increasing threat of salinity are adversely affecting rice productivity in the southern coastal lands of Bangladesh. A Bangladeshi rice landrace Horkuch, adapted to these saline conditions, has long been cultivated by farmers in this region. To understand the trend and heritability of its tolerance traits, a reciprocal population of Horkuch with the high-yielding sensitive rice IR29 was generated for mapping of quantitative trait loci (QTLs) at both seedling and reproductive stages in an F2:3 strategy using double-digest restriction associated DNA. We found 29 QTLs and some QTL clusters containing survival and yield-related QTLs showing pleiotropic effects over some phenotypes. We advanced the generation up to F5 to obtain homozygosity and our current work is aimed at confirming these mapped QTLs at F5 by salt stress physiological tests at both stages as well as DNA markers linked to these QTLs. We confirmed SES QTL (survival of seedling under stress) associated with SSR marker RM25789 and two QTL clusters at chromosome 10 and 11 associated with RM26964 and RM27027, respectively. One cluster harbored yield-related filled grain number, filled grain weight, total grain number, harvest index, ionic balance and transpiration-related total sodium, total potassium and stomatal conductance QTLs. The other cluster contained total grain weight, filled grain weight and seedling root relative water content QTLs. We identified some individuals based on their physiological performance under stress as well as the presence of QTLs associated with some SSR markers that can be used for breeding and production of highly salt-tolerant cultivars with high yield.