Analyzing Quantitative Trait Loci for Fiber Quality and Yield-Related Traits From a Recombinant Inbred Line Population With Gossypium hirsutum Race palmeri as One Parent

Fiber quality and yield-related traits are important agronomic traits in cotton breeding. To detect the genetic basis of fiber quality and yield related traits, a recombinant inbred line (RIL) population consisting of 182 lines was established from a cross between Gossypium hirsutum cultivar CCRI35 and G. hirsutum race palmeri accession TX-832. The RIL population was deeply genotyped using SLAF-seq and was phenotyped in six environments. A high-density genetic linkage map with 15,765 SNP markers and 153 SSR markers was constructed, with an average distance of 0.30 cM between adjacent markers. A total of 210 fiber quality quantitative trait loci (QTLs) and 73 yield-related QTLs were identified. Of the detected QTLs, 62 fiber quality QTLs and 10 yield-related QTLs were stable across multiple environments. Twelve and twenty QTL clusters were detected on the At and Dt subgenome, respectively. Twenty-three major QTL clusters were further validated through associated analysis and five candidate genes of four stable fiber quality QTLs were identified. This study revealed elite loci influencing fiber quality and yield and significant phenotypic selection regions during G. hirsutum domestication, and set a stage for future utilization of molecular marker assisted breeding in cotton breeding programs.

Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson’s correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.

Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

Background The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production. Methods Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used. Results Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006–JD1007 and RM1148–RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.

Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers

Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.

Quantitative Trait Locus Mapping for Drought Tolerance in Soybean Recombinant Inbred Line Population

Improving drought stress tolerance of soybean could be an effective way to minimize the yield reduction in the drought prevailing regions. Identification of drought tolerance-related quantitative trait loci (QTLs) is useful to facilitate the development of stress-tolerant varieties. This study aimed to identify the QTLs for drought tolerance in soybean using a recombinant inbred line (RIL) population developed from the cross between a drought-tolerant ‘PI416937’ and a susceptible ‘Cheonsang’ cultivar. Phenotyping was done with a weighted drought coefficient derived from the vegetative and reproductive traits. The genetic map was constructed using 2648 polymorphic SNP markers that distributed on 20 chromosomes with a mean genetic distance of 1.36 cM between markers. A total of 10 QTLs with 3.52–4.7 logarithm of odds value accounting for up to 12.9% phenotypic variance were identified on seven chromosomes. Five chromosomes—2, 7, 10, 14, and 20—contained one QTL each, and chromosomes 1 and 19 harbored two and three QTLs, respectively. The chromosomal locations of seven QTLs overlapped or located close to the related QTLs and/or potential candidate genes reported earlier. The QTLs and closely linked markers could be utilized in maker-assisted selection to accelerate the breeding for drought tolerance in soybean.