Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress

Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice

Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (p< 0.0001) for culm strength traits. Two novel major effect marker-trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the indica background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice.

Superior haplotypes of key drought-responsive genes reveal opportunities for the development of climate-resilient rice varieties

Haplotype-based breeding is an emerging and innovative concept that enables the development of designer crop varieties by exploiting and exploring superior alleles/haplotypes among target genes to create new traits in breeding programs. In this regard, whole-genome re-sequencing of 399 genotypes (landraces and breeding lines) from the 3000 rice genomes panel (3K-RG) is mined to identify the superior haplotypes for 95 drought-responsive candidate genes. Candidate gene-based association analysis reveals 69 marker-trait associations (MTAs) in 16 genes for single plant yield (SPY) under drought stress. Haplo-pheno analysis of these 16 genes identifies superior haplotypes for seven genes associated with the higher SPY under drought stress. Our study reveals that the performance of lines possessing superior haplotypes is significantly higher (p ≤ 0.05) as measured by single plant yield (SPY), for the OsGSK1-H4, OsDSR2-H3, OsDIL1-H22, OsDREB1C-H3, ASR3-H88, DSM3-H4 and ZFP182-H4 genes as compared to lines without the superior haplotypes. The validation results indicate that a superior haplotype for the DREB transcription factor (OsDREB1C) is present in all the drought-tolerant rice varieties, while it was notably absent in all susceptible varieties. These lines carrying the superior haplotypes can be used as potential donors in haplotype-based breeding to develop high-yielding drought-tolerant rice varieties.

Mapping of QTLs and meta-QTLs for Heterodera avenae Woll. resistance in common wheat (Triticum aestivum L.)

BACKGROUND

In hexaploid wheat, quantitative trait loci (QTL) and meta-QTL (MQTL) analyses were conducted to identify genomic regions controlling resistance to cereal cyst nematode (CCN), Heterodera avenae. A mapping population comprising 149 RILs derived from the cross HUW 468 × C 306 was used for composite interval mapping (CIM) and inclusive composite interval mapping (ICIM).

RESULTS

Eight main effect QTLs on three chromosomes (1B, 2A and 3A) were identified using two repeat experiments. One of these QTLs was co-localized with a previously reported wheat gene Cre5 for resistance to CCN. Seven important digenic epistatic interactions (PVE = 5% or more) were also identified, each involving one main effect QTL and another novel E-QTL. Using QTLs earlier reported in literature, two meta-QTLs were also identified, which were also used for identification of 57 candidate genes (CGs). Out of these, 29 CGs have high expression in roots and encoded the following proteins having a role in resistance to plant parasitic nematodes (PPNs): (i) NB-ARC,P-loop containing NTP hydrolase, (ii) Protein Kinase, (iii) serine-threonine/tyrosine-PK, (iv) protein with leucine-rich repeat, (v) virus X resistance protein-like, (vi) zinc finger protein, (vii) RING/FYVE/PHD-type, (viii) glycosyl transferase, family 8 (GT8), (ix) rubisco protein with small subunit domain, (x) protein with SANT/Myb domain and (xi) a protein with a homeobox.

CONCLUSION

Identification and selection of resistance loci with additive and epistatic effect along with two MQTL and associated CGs, identified in the present study may prove useful for understanding the molecular basis of resistance against H. avenae in wheat and for marker-assisted selection (MAS) for breeding CCN resistant wheat cultivars.

QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population

Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.

Transgenerational effects of chromium stress at the phenotypic and molecular level in Arabidopsis thaliana

In this study, we describe the results obtained in a study of the transgenerational phenotypic effects of chromium (Cr) stress on the model plant species Arabidopsis thaliana. The F1 generation derived from parents grown under chronic and medium chronic stress showed significantly higher levels of the maximal effective concentration (EC₅₀) compared with F1 plants generated from unstressed parents. Moreover, F1 plants from Cr-stressed parents showed a higher germination rate when grown in the presence of Cr. F1 plants derived from parents cultivated under chronic Cr stress displayed reduced hydrogen peroxide levels under Cr stress compared to controls. At lower Cr stress levels, F1 plants were observed to activate promptly more genes involved in Cr stress responses than F0 plants, implying a memory effect linked to transgenerational priming. At higher Cr levels, and at later stages, F1 plants modulated significantly fewer genes than F0 plants, implying a memory effect leading to Cr stress adaptation. Several bHLH transcription factors were induced by Cr stress in F1 but not in F0 plants, including bHLH100, ORG2 and ORG3. F1 plants optimized gene expression towards pathways linked to iron starvation response. A model of the transcriptional regulation of transgenerational memory to Cr stress is presented here, and could be applied for other heavy metal stresses.

Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice (Oryza sativa L.)

The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.

DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds

The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential. By modeling the transcriptional networks across sibling qDTY12.1-introgression lines with contrasting yield under drought (LPB = low-yield penalty; HPB = high-yield penalty), the qDTY12.1-encoded DECUSSATE gene (OsDEC) was revealed as the core of a synergy with other genes in the genetic background. OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway. Results support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. The functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the drought-induced depletion of photosynthate needed for reproductive growth. Its impact is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought.

R, Phani Padmakumari A, Singh VK, Kumar A. Marker-assisted forward and backcross breeding for improvement of elite Indian rice variety Naveen for multiple biotic and abiotic stress tolerance

The elite Indian rice variety, Naveen is highly susceptible to major biotic and abiotic stresses such as blast, bacterial blight (BB), gall midge (GM) and drought which limit its productivity in rainfed areas. In the present study, a combined approach of marker-assisted forward (MAFB) and back cross (MABC) breeding was followed to introgress three major genes, viz., Pi9 for blast, Xa21 for bacterial blight (BB), and Gm8 for gall midge (GM) and three major QTLs, viz., qDTY_1.1, qDTY_2.2 and qDTY_4.1 conferring increased yield under drought in the background of Naveen. At each stage of advancement, gene-based/linked markers were used for the foreground selection of biotic and abiotic stress tolerant genes/QTLs. Intensive phenotype-based selections were performed in the field for identification of lines with high level of resistance against blast, BB, GM and drought tolerance without yield penalty under non-stress situation. A set of 8 MAFB lines and 12 MABC lines with 3 to 6 genes/QTLs and possessing resistance/tolerance against biotic stresses and reproductive stage drought stress with better yield performance compared to Naveen were developed. Lines developed through combined MAFB and MABC performed better than lines developed only through MAFB. This study exemplifies the utility of the combined approach of marker-assisted forward and backcrosses breeding for targeted improvement of multiple biotic and abiotic stress resistance in the background of popular mega varieties.

Genomics-assisted breeding for successful development of multiple-stress-tolerant, climate-smart rice for southern and southeastern Asia

Rice (Oryza sativa L.) in rainfed marginal environments is prone to multiple abiotic and biotic stresses, which can occur in combination in a single cropping season and adversely affect rice growth and yield. The present study was undertaken to develop high-yielding, climate-resilient rice that can provide tolerance to multiple biotic and abiotic stresses. An assembled first-crossing scheme was employed to transfer 15 quantitative trait loci (QTL) and genes-qDTY_1.1 , qDTY_2.1 , qDTY_3.1 , qDTY_12.1 (drought), Sub1 (submergence), Gm4 (gall midge), Pi9, Pita2 (blast), Bph3, Bph17 (brown plant hoppers), Xa4, xa5, xa13, Xa21, and Xa23 (bacterial leaf blight)-from eight different parents using genomics-assisted breeding. A funnel mating design was employed to assemble all the targeted QTL and genes into a high-yielding breeding line IR 91648-B-1-B-3-1. Gene-based linked markers were used in each generation from intercrossing to the F₆ generation for tracking the presence of desirable alleles of targeted QTL and genes. Single-plant selections were performed from F₂ onwards to select desirable recombinants possessing alleles of interest with suitable phenotypes. Phenotyping of 95 homozygous F₆ lines carrying six to 10 QTL and genes was performed for nonstress, reproductive-stage (RS) drought, blast, bacterial leaf blight (BLB), gall midge (GM), and for grain quality parameters such as chalkiness, amylose content (AC), gelatinization temperature (GT), and head rice recovery (HRR). Finally, 56 F₇ homozygous lines were found promising for multiple-location evaluation for grain yield (GY) and other traits. These multiple-stress-tolerant lines with the desired grain quality profiling can be targeted for varietal release in southern and southeastern Asia through national release systems.

Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) “Axiom_Arachis” array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004–2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0–33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases; malate dehydrogenases; microtubule-associated proteins; and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.

Utilization of genetic diversity and marker-trait to improve drought tolerance in rice (Oryza sativa L.)

Drought stress is one of the main problems for the rice crop, as it reduces the production and productivity of the grain yield significantly. In Egypt, many restrictions were made on the cultivation of rice due to its high-water demand. Producing promising drought-tolerant rice cultivars combined with high yielding is one of the main targets for rice breeders. A set of 22 highly diverse rice genotypes were evaluated under normal and drought conditions. Morphological, physiological, and yield traits were recorded on each genotype. Drought susceptibility index (DSI) was estimated for six yield traits to identify the most drought-tolerant rice genotypes. A high genetic variation was found among genotypes tested in the experiment. Under normal conditions, the highest phenotypic correlation was found between grain yield (GY) and sterility percentage (SP) (- 0.73**), while it was among GY and chlorophyll content (CC) (0.82**) under drought conditions. To identify quantitative trait loci (QTL) controlling yielding traits under drought and normal, a single marker analysis was performed between all yield traits under both conditions and a set of 106 simple sequence repeat (SSR) marker alleles. The genetic association analysis revealed 14 and 17 QTL under drought and normal conditions, respectively. The most drought-tolerant genotypes were selected based on phenotypic traits, the number of QTL in each selected genotype, and the level of genetic diversity existed among the genotypes. As a result, five genotypes (Giza 178, IET1444, GZ1368-S-5-4, Nahda, Giza 14) were identified as the most promising drought-tolerant rice genotypes. Eight QTL controlling drought tolerance were identified in Giza 178, Nahda, and GZ1368-S-5-4, while four QTL were found in IET1444. The number of different QTLs were estimated among the five selected genotypes. Giza 178 and GZ1368-S-5-4 shared the same QTLs. Seven different QTLs were found among Nahda, IET1444, GZ1368-S-5-4, and Giza 14. Combining information from phenotypic traits, genetic diversity analysis, and QTL analysis was very useful in identifying the true drought-tolerant rice genotypes that can be used for crossing in the future breeding program.

More and more of less and less: Is genomics-based breeding of dry direct-seeded rice (DDSR) varieties the need of hour?

Rice is a staple food for half of the world's population. Changing climatic conditions, water and labour scarcity are the major challenges that shall limit future rice production. Dry direct-seeded rice (DDSR) is emerging as an efficient, resources conserving, mechanized, climate smart and economically viable strategy to be adopted as an alternative to puddled transplanted rice (TPR) with the potential to address the problem of labour-water shortages and ensure sustainable rice cultivation. Despite these benefits, several constraints obstruct the adoption of DDSR. In principle, the plant type for DDSR should be different from one for TPR, which could be achieved by developing rice varieties that combine the traits of upland and lowland varieties. In this context, recent advances in precise phenotyping and NGS-based trait mapping led to identification of promising donors and QTLs/genes for DDSR favourable traits to be employed in genomic breeding. This review discusses the important traits influencing DDSR, research studies to clarify the need for breeding DDSR-specific varieties to achieve enhanced grain yield, climate resilience and nutrition demand. We anticipate that in the coming years, genomic breeding for developing DDSR-specific varieties would be a regular practice and might be further strengthened by combining superior haplotypes regulating important DDSR traits by haplotype-based breeding.

Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel

BACKGROUND

Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers.

RESULTS

The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought.

CONCLUSION

These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.

Development of introgression lines in high yielding, semi-dwarf genetic backgrounds to enable improvement of modern rice varieties for tolerance to multiple abiotic stresses free from undesirable linkage drag

Occurrence of multiple abiotic stresses in a single crop season has become more frequent than before. Most of the traditional donors possessing tolerance to abiotic stresses are tall, low-yielding with poor grain quality. To facilitate efficient use of complex polygenic traits in rice molecular breeding research, we undertook development of introgression lines in background of high-yielding, semi-dwarf varieties with good grain quality. The study reports the development and evaluations of over 25,000 introgression lines in eleven elite rice genetic backgrounds for improvement of yield under multiple abiotic-stresses such as drought, flood, high/low temperature. The developed introgression lines within each genetic background are near isogenic/recombinant inbred lines to their recipient recurrent parent with 50 to 98% background recovery and additionally carry QTLs/genes for abiotic stresses. The multiple-stress tolerant pyramided breeding lines combining high yield under normal situation and good yield under moderate to severe reproductive-stage drought, semi-dwarf plant type with good grain quality traits have been developed. The introgression lines in dwarf backgrounds open new opportunity to improve other varieties without any linkage drag as well as facilitate cloning of QTLs, identification and functional characterization of candidate genes, mechanisms associated with targeted QTLs and the genetic networks underlying complex polygenic traits.

Marker Assisted Forward Breeding to Combine Multiple Biotic-Abiotic Stress Resistance/Tolerance in Rice

BACKGROUND

Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (Pi9), bacterial leaf blight (BLB) (Xa4, xa5, xa13, Xa21), brown planthopper (BPH) (Bph3, Bph17), gall midge (GM) (Gm4, Gm8) and QTLs for drought tolerance (qDTY_1.1 and qDTY_3.1) through marker-assisted forward breeding (MAFB) approach.

RESULT

Seven introgression lines (ILs) possessing a combination of seven to ten genes/QTLs for different biotic and abiotic stresses have been developed using marker-assisted selection (MAS) breeding method in the background of Swarna with drought QTLs. These ILs were superior to the respective recurrent parent in agronomic performance and also possess preferred grain quality with intermediate to high amylose content (AC) (23-26%). Out of these, three ILs viz., IL1 (Pi9+ Xa4+ xa5+ Xa21+ Bph17+ Gm8+ qDTY_1.1+ qDTY_3.1), IL6 (Pi9+ Xa4+ xa5+ Xa21+ Bph3+ Bph17+ Gm4+ Gm8+ qDTY_1.1+ qDTY_3.1) and IL7 (Pi9+ Xa4+ xa5+ Bph3+ Gm4+ qDTY_1.1+ qDTY_3.1) had shown resistance\tolerance for multiple biotic and abiotic stresses both in the field and glasshouse conditions. Overall, the ILs were high yielding under various stresses and importantly they also performed well in non-stress conditions without any yield penalty.

CONCLUSION

The current study clearly illustrated the success of MAS in combining tolerance to multiple biotic and abiotic stresses while maintaining higher yield potential and preferred grain quality. Developed ILs with seven to ten genes in the current study showed superiority to recurrent parent Swarna+drought for multiple-biotic stresses (blast, BLB, BPH and GM) together with yield advantages of 1.0 t ha^- 1 under drought condition, without adverse effect on grain quality traits under non-stress.

Identification and Validation of Aerobic Adaptation QTLs in Upland Rice

The aerobic adaptation of upland rice is considered as the key genetic difference between upland rice and lowland rice. Genetic dissection of the aerobic adaptation is important as the basis for improving drought tolerance and terrestrial adaptation by using the upland rice. We raised BC₁-BC₃ introgression lines (ILs) in lowland rice Minghui 63 (MH63) background. The QTLs of yield and yield-related traits were detected based on ILs under the aerobic and lowland environments, and then the yield-related QTLs were identified in a backcrossed inbred population of BC₄F₅ under aerobic condition. We further verified phenotypes of QTL near-isogenic lines. Finally, three QTLs responsible for increasing yield in aerobic environment were detected by multiple locations and generations, which were designated as qAER1, qAER3, and qAER9 (QTL of aerobic adaptation). The qAER1 and qAER9 were fine-mapped. We found that qAER1 and qAER9 controlled plant height and heading date, respectively; while both of them increased yields simultaneously by suitable plant height and heading date without delay in the aerobic environment. The phenotypic differences between lowland rice and upland rice in the aerobic environment further supported the above results. We pyramided the two QTLs as corresponding molecular modules in the irrigated lowland rice MH63 background, and successfully developed a new upland rice variety named as Zhongkexilu 2. This study will lay the foundation for using aerobic adaptation QTLs in rice breeding programs and for further cloning the key genes involved in aerobic adaptation.

Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross

Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC2F8 generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.

Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross

The genetic gain in yield and quality are two major targets of wheat breeding programs around the world. In this study, a high density genetic map consisting of 10,172 SNP markers identified a total of 43 genomic regions associated with three quality traits, three yield traits and two agronomic traits in hard red spring wheat (HRSW). When compared with six grain shape and size traits, the quality traits showed mostly independent genetic control (~18% common loci), while the yield traits showed moderate association (~53% common loci). Association of genomic regions for grain area (GA) and thousand-grain weight (TGW), with yield suggests that targeting an increase in GA may help enhancing wheat yield through an increase in TGW. Flour extraction (FE), although has a weak positive phenotypic association with grain shape and size, they do not share any common genetic loci. A major contributor to plant height was the Rht8 locus and the reduced height allele was associated with significant increase in grains per spike (GPS) and FE, and decrease in number of spikes per square meter and test weight. Stable loci were identified for almost all the traits. However, we could not find any QTL in the region of major known genes like GPC-B1, Ha, Rht-1, and Ppd-1. Epistasis also played an important role in the genetics of majority of the traits. In addition to enhancing our knowledge about the association of wheat quality and yield with grain shape and size, this study provides novel loci, genetic information and pre-breeding material (combining positive alleles from both parents) to enhance the cultivated gene pool in wheat germplasm. These resources are valuable in facilitating molecular breeding for wheat quality and yield improvement.