Quantitative trait locus mapping for seed artificial aging traits using an F2:3 population and a recombinant inbred line population crossed from two highly related maize inbreds

Quantitative trait locus (QTL) mapping for seed longevity is essential for breeding modern cultivars with resistance to deterioration during postharvest storage. The inbred lines X178 and I178 showed large differences in seed vigour after artificial aging treatment, while they had similar performances in terms of most agronomic traits. An F_2:3 population and a recombinant inbred line (RIL) population were generated to map QTL after 5 days under artificial aging conditions. Positive correlations were observed among all investigated traits including the aging germination rate, relative aging germination rate, aging simple vigour index, aging primary root length, aging shoot length and aging total length. Thirteen QTL were identified to locate on five chromosome regions: Chr.1:297 Mb (chromosome 1 region 297 Mb), Chr.3:205 Mb, Chr.4:240 Mb, Chr.5:205 Mb and Chr.7:155 Mb, with 2 to 4 QTL co‐located on a region. In each region, 3–8 previously identified aging‐related QTL were located, confirming the importance of these regions for controlling seed longevity in different maize populations. Taken together, the results of this work provide a foundation for further QTL fine mapping and the molecular‐assisted breeding of aging tolerant maize.     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

Genetic analysis and QTL mapping of oil content and seed index using two recombinant inbred lines and two backcross populations in Upland cotton

Cottonseed is one of the main by‐products of cotton. To explore the genetic composition of oil content (OC) and seed index (SI) is helpful for utilizing the cottonseed. Under multiple environmental conditions, the genetic structures of OC and SI were explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations in Upland cotton. Twenty‐four and 31 quantitative trait loci (QTLs) for OC and SI, respectively, were detected using composite interval mapping, in which 9 QTLs for OC and 18 QTLs controlling SI were simultaneously identified in more than two environments or two populations. Forty‐seven and 37 QTLs with main effects (M‐QTLs) for OC and SI and 114 and 74 QTLs involved in digenic interactions (E‐QTLs), respectively, identified by inclusive composite interval mapping. On average, the E‐QTLs explained a larger portion of the phenotypic variation than the M‐QTLs did. It was concluded that additive effects of single‐locus and epistasis derived from complementary loci with few detectable single‐locus effects played an important role in oil content and seed index in Upland cotton.     

Inheritance of Striga hermonthica adaptive traits in an early‐maturing white maize inbred line containing resistance genes from Zea diploperennis

Striga hermonthica can cause as high as 100% yield loss in maize depending on soil fertility level, type of genotype, severity of infestation and climatic conditions. Understanding the mode of inheritance of Striga resistance in maize is crucial for introgression of resistance genes into tropical germplasm and deployment of resistant varieties. This study examined the mode of inheritance of resistance to Striga in early‐maturing inbred line, TZdEI 352 containing resistance genes from Zea diploperennis. Six generations, P₁, P₂, F₁, F₂, BC₁P₁ and BC₁P₂ derived from a cross between resistant line, TZdEI 352 and susceptible line, TZdEI 425 were screened under artificial Striga infestation at Mokwa and Abuja, Nigeria, 2015. Additive‐dominance model was adequate in describing observed variations in the number of emerged Striga plants among the population; hence, digenic epistatic model was adopted for Striga damage. Dominance effects were higher than the additive effects for the number of emerged Striga plants at both locations signifying that non‐additive gene action conditioned inheritance of Striga resistance. Inbred TZdEI 352 could serve as invaluable parent for hybrid development in Striga endemic agro‐ecologies of sub‐Saharan Africa.     

Genetic dissection of vitamin E content in rice (Oryza sativa) grains using recombinant inbred lines derived from a cross between 'Zhenshan97B' and 'Nanyangzhan'

Vitamin E (VE) is an important nutritional trait in rice grains. In order to dissect the genetic basis underlying VE content, a recombinant inbred lines population derived from 'Zhenshan 97B' and 'Nanyangzhan' was used for quantitative trait locus (QTL) analysis. Totally, 29 QTLs for six VE traits were identified in 2 consecutive years. Among those, five QTLs repeatedly detected in two years formed a cluster on chromosome 2, which was responsible for all five VE isomers. OsγTMT, the gene encoding γ‐tocopherol methyltransferase in rice, was located to the same region and treated as the candidate gene. Sequence analysis of alleles from two parents revealed many polymorphisms, including 19 single nucleotide polymorphisms (SNPs) and two insert/deletions (Indels) in the promoter region, two nonsynonymous SNPs in exons, and 25 SNPs and an Indel in introns. Besides, a QTL for δ‐tocotrienol and two QTLs for α‐tocopherol were repeatedly detected on chromosome 5 and 8, respectively, all three regions carrying no homologous genes involved in VE biosynthesis. These results could be useful in development of rice lines displaying desirable VE content.     

Genetic dissection of seed storability using two different populations with a same parent rice cultivar N22

Seed storability in rice (Oryza sativa L.) is an important agronomic trait. Two segregating populations with N22 (indica) as a common parent, viz. a set of 122 backcross-inbred lines (BILs) derived from the backcross Nanjing35 (japonica)/N22//Nanjing35 and another population comprising 189 recombinant inbred lines (RILs) from the cross of USSR5 (japonica) and N22, were studied to detect quantitative trait loci (QTL) controlling seed storability. Germination percentage (GP) was used to evaluate seed storability after aging treated under three different conditions, viz. natural, artificial and combined aging treatments. A total of seven QTLs were identified on chromosomes 1, 2, 5, 6 and 9. Among them, a major QTL, qSSn-9, was common in the two populations. In contrast, four QTLs (qSSnj-2-1, qSSn-2-2, qSSn-5 and qSSn-6) were detected in BILs and the QTL qSSn-1 was identified in RILs, which was a new QTL for seed storability. The N22-derived alleles increased the seed storability at all the loci except qSSnj-2-1. We also investigated the effect of QTLs using five selected lines with high storability from BILs and verified qSSn-5 with a near-isogenic line (NIL). These results provide an opportunity for pyramiding or map-based cloning major QTLs for seed storability in rice.     

Genetic diversity of tropical maize inbred lines combining resistance to Striga hermonthica with drought tolerance using SNP markers

Striga hermonthica and drought are the major stresses limiting maize yields in sub‐Saharan Africa. The search for diverse maize lines’ tolerance to drought and resistance to S. hermonthica (DTSTHR) is very crucial for yield improvement in areas affected by the two stresses. Understanding the genetic diversity among the lines is important to develop cultivars resistant to S. hermonthica and tolerant to drought. The lines were developed from biparental crosses of drought‐tolerant and Striga‐resistant lines. A total of 128 DTSTHR maize lines were characterized using single‐nucleotide polymorphism (SNP) markers. Results of the cluster analysis based on 3297 SNP markers showed four distinct groups consistent with the pedigrees of the lines. Furthermore, model‐based analysis also formed the same groups of the DTSTHR lines. Integrating the pedigree information with combining ability and the SNP analyses may provide defined heterotic groups for maize improvement work in West and Central Africa. These results also help breeders to utilize DTSTHR lines present at IITA for developing biparental crosses without disrupting the heterotic groups they have established in their breeding programmes.     

Identification and validation of an over‐dominant QTL controlling soybean seed weight using populations derived from Glycine max × Glycine soja

Heterosis, or hybrid vigour, has been used to improve seed yield in several important crops for decades and it has potential applications in soybean. The discovery of over‐dominant quantitative trait loci (QTL) underlying yield‐related traits, such as seed weight, will facilitate hybrid soybean breeding via marker‐assisted selection. In this study, F₂ and F_2 : 3 populations derived from the crosses of ‘Jidou 12’ (Glycine max) × ‘ZYD2738’ (Glycine soja) and ‘Jidou 9’ (G. max) × ‘ZYD2738’ were used to identify over‐dominant QTL associated with seed weight. A total of seven QTL were identified. Among them, qSWT_13_1, mapped on chromosome 13 and linked with Satt114, showed an over‐dominant effect in two populations for two successive generations. This over‐dominant effect was further examined by six subpopulations derived from ‘Jidou12’ × ‘ZYD2738’. The seed weight for heterozygous individuals was 1.1‐ to 1.6‐fold higher than that of homozygous individuals among the six validation populations examined in different locations and years. Therefore, qSWT_13_1 may be a useful locus to improve the yield of hybrid soybean and to understand the molecular mechanism of heterosis in soybean.