QTL mapping for agronomic and fibre traits using two interspecific chromosome substitution lines of Upland cotton

CS‐B14Sh and CS‐B22Sh are cotton interspecific chromosome substitution (CS)‐B lines, in which a pair of short arms of chromosome 14 and chromosome 22 were introgressed from Gossypium barbadense doubled‐haploid line 3‐79 with the background of Gossypium hirsutum line TM‐1, respectively. These two CS‐B lines were crossed with TM‐1, and segregating progenies (F₂ and F_2:3, respectively) were obtained. Phenotypic data of lint yield, yield‐related traits and fibre‐quality traits were collected from two trials. In the cross CS‐B14SH X TM‐1, QTL for boll weight (BW), lint percentage (LP), fibre upper half mean length (UHML), micronaire reading (MIC), and fibre breaking tensile strength (STR) were repeatedly detected. Alleles from 3‐79 decreased BW and MIC, but increased UHML and STR. In the cross CS‐B22Sh X TM‐1, QTL for BW, LP, UHML, MIC, STR, fibre elongation (EL),seed weight(SW), node of first fruiting branch (NFB) and fibre uniformity index (UI) were repeatedly detected, and alleles from 3‐79 decreased UHML, UI and STR, but increased NFB, SW, MIC and EL. QTL clusters were found in both populations.     

Fine mapping the QTL qFS‐chr.23, using a CSIL

In an earlier advanced‐backcross quantitative trait locus (QTL) analysis of an interspecific cross of Gossypium hirsutum cv. ‘Xinluzhong 36’(‘XLZH36’) and G. barbadense cv. ‘Xinhai 21’(‘XH21’), a QTL for fibre strength in the chromosome segment introgression line IL23‐09 was analysed. Single marker analysis revealed that the markers on chro.23 were associated with fibre strength. Using composite interval mapping with the F₂ population (1296 plants), a QTL for fibre strength was detected on chro. 23. The QTL explained 8.9% and 15.9% of phenotypic variances in the F₂ and F_2 : 3 generations, respectively. Substitution mapping suggested that the QTL was located at a physical distance of 23.4 kb between the markers BNL1414 and the single nucleotide polymorphism (SNP) locus D09_43776813 C‐G. We designated this QTL as qFS‐chr.23 (quantitative trait locus for fibre strength on chro.23). This work provides a valuable genetic resource for the breeding of high fibre quality in cotton and will facilitate future efforts for map‐based cloning.     

Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPD

Tetraploid cotton is one of the most extensively cultivated species. Two tetraploid species, Gossypium hirsutum L. and G. barbadense L., dominate the world's cotton production. To better understand the genetic basis of cotton fibre traits for the improvement of fibre quality, a genetic linkage map of tetraploid cotton was constructed using sequence‐related amplified polymorphisms (SRAPs), simple sequence repeats (SSRs) and random amplified polymorphic DNAs (RAPDs). A total of 238 SRAP primer combinations, 368 SSR primer pairs and 600 RAPD primers were used to screen polymorphisms between G. hirsutum cv. Handan208 and G. barbadense cv. Pima90 which revealed 749 polymorphic loci in total (205 SSRs, 107 RAPDs and 437 SRAPs). Sixty‐nine F₂ progeny from the interspecific cross of ‘Handan208’בPima90’ were genotyped with the 749 polymorphic markers. A total of 566 loci were assembled into 41 linkage groups with at least three loci in each group. Twenty‐eight linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 5141.8 cM with a mean interlocus space of 9.08 cM. A × test for significance of deviations from the expected ratio (1: 2: 1 or 3: 1) identified 135 loci (18.0%) with skewed segregation, most of which had an excess of maternal parental alleles. In total, 13 QTL associated with fibre traits were detected, among which two QTL were for fibre strength, four for fibre length and seven for micronaire value. These QTL were on nine linkage groups explaining 16.18‐28.92% of the trait variation. Six QTL were located in the A subgenome, six QTL in the D subgenome and one QTL in an unassigned linkage group. There were three QTL for micronaire value clustered on LG1, which would be very useful for improving this trait by molecular marker‐assisted selection.     

Genetic analysis of agronomic and fibre traits using four interspecific chromosome substitution lines in cotton

Backcrossed chromosome substitution lines (CS‐B) have been developed with a homologous pair of chromosomes or chromosome arms of Gossypium barbadense (3‐79) germplasm substituted for the homologous Gossypium hirsutum(TM‐1) chromosomes or chromosome segments. We report on agronomic and fibre trait performance of four backcrossed chromosome or chromosome arm substitution lines including chromosomes 01, 11sh (chromosome 11 short arm), 12 sh and 26 Lo (chromosome 26 long arm). Data for agronomic and fibre traits were collected from replicated field experiments at two different locations in 2 years, and analysed under an additive dominance genetic model. CS‐B 12sh had higher, while CS‐B 01 and CS‐B 26Lo had lower boll weight than TM‐1. The presence of significant negative additive effects for micronaire with CS‐B 01 and significant positive additive effects for elongation and fibre strength with CS‐B 11sh suggested the substituted chromosome arms of 3‐79 in these CS‐B lines were more likely carrying genes causing these effects. Results revealed that several CS‐B lines had significant homozygous and heterozygous dominance effects for different agronomic and fibre traits suggesting that specific CS‐B lines may be useful for improving agronomic and fibre traits in hybrid cottons. These CS‐B lines also provide novel genetic resources for improving upland cotton germplasm.     

Effects of the dominant glandless gene Gl2e on agronomic and fibre characters of Upland cotton

Seven pairs of near‐isogenic lines (glandless vs. glanded) and the recurrent parents were used to determine the effects of the dominant glandless gene from ‘Hai 1’(Gossypium barbadense) on agronomic, fibre, and seed characters in Upland cotton, Gossypium hirsutum, backgrounds. The results showed that there were no apparent linkage associations of the glandless gene on most agronomic, fibre and seed characters of Upland cotton, except for seed quality. The glandless line derived from ‘Liaomian 7’had significantly more protein (489.6 g/kg), and that from H237 had significantly more oil (362.4 g/kg) and had the largest oil index (2.70 g) and protein index (3.03 g). The gossypol content of seed in dominant glandless lines in Upland cotton was very low (<0.04 g/kg). Therefore, it is suggested that the glandless gene can play an important role in breeding glandless or low seed‐gossypol Upland cotton cultivars.     

Genetic association of within‐boll yield components and boll morphological traits with fibre properties in upland cotton (Gossypium hirsutum L.)

Knowledge of genetic relationships between within‐boll yield components and fibre quality is essential for simultaneous improvement of lint yield and fibre quality in upland cotton (Gossypium hirsutum L.). Nine parents and their F₁ progeny with reciprocals from a 3 × 6 factorial mating design were grown in 2008 and 2009. Seven within‐boll yield components and two boll morphological traits and the three fibre quality parameters were analysed based on a conditional additive/dominance (AD) genetic model. Results showed that boll length contributed to the largest proportion of phenotypic, additive and dominance variances for UHM length; seed index contributed to the largest proportion of phenotypic and additive variances for fibre strength; boll width made the largest contribution to phenotypic and additive variances and the second largest contribution to dominance‐by‐environment interaction variance for micronaire, indicating that they played an important role than the other traits for fibre length, strength and fineness/maturity, respectively. It is worthy of note that those correlations between boll shape and fibre quality apply only to the nine parents and the resultant hybrids in this study and do not imply a cause and effect relationship.     

Construction of high‐throughput genotyped chromosome segment substitution lines in rice (Oryza sativa L.) and QTL mapping for heading date

Chromosome segment substitution lines (CSSLs) provide ideal materials for quantitative trait loci (QTLs) mapping and genetic dissection of complex traits. In this study, we developed a set of CSSL population consisting of 175 lines, which were derived between the recipient ‘Guangluai 4’ and the donor ‘Nipponbare’. Based on 260 molecular markers, we firstly constructed a physical map of core 97 lines. Then, these 97 lines were further genotyped based on resequencing data, and a resequencing‐based physical map was constructed. Compared with the molecular marker‐based physical map, the resequencing‐based physical map of 97 lines contained 367 substituted segments with 252 newly discovered segments. The total size of the 367 substituted segments was 1,074 Mb, which was 2.81 times the size of rice genome. Using the 97 CSSLs as materials, we identified nine QTLs for heading date and three of them were firstly reported. All the QTLs had positive additive effects, ranging from 9.50 to 16.50 days. These CSSLs may greatly help forge a new resource for functional genomics studies and molecular breeding in rice.     

Fine mapping of a QTL for the number of spikelets per panicle by using near‐isogenic lines derived from an interspecific cross between Oryza sativa and Oryza minuta

We constructed a high‐resolution physical map for the qSPP7 QTL for spikelets per panicle (SPP) on rice chromosome 7 across a 28.6‐kb region containing four predicted genes. Using a series of BC₇F₄ near‐isogenic lines (NILs) derived from a cross between the Korean japonica cultivar ‘Hwaseongbyeo’ and Oryza minuta (IRGC Acc. No. 101144), three QTLs for the number of SPP, grains per panicle and primary branches were identified in the cluster (P ≤ 0.01). All three QTLs were additive, and alleles from the O. minuta parent were beneficial in the ‘Hwaseongbyeo’ background. qSPP7 was mapped to a 28.6‐kb region between the two simple sequence repeat (SSR) markers RM4952 and RM21605. The additive effect of the O. minuta allele at qSPP7 was 23 SPP, and 43.6% of the phenotypic variance was explained by the segregation of the SSR marker RM4952. Colocalization of the three QTLs suggested that this locus was associated with panicle structure and had pleiotropic effects. The NIL populations and molecular markers are useful for cloning qspp7.     

QTL mapping for seedling traits associated with low‐nitrogen tolerance using a set of advanced backcross introgression lines of rice

Nitrogen (N) deficiency is a major yield‐limiting factor in rice production. The objective of this study was to identify putative QTLs for low‐N stress tolerance of rice, using an advanced backcross population derived from crosses between an indica cultivar ‘93‐11’ and a japonica cultivar ‘Nipponbare’ and genotyped at 250 marker loci. Plant height, maximum root length, root dry weight, shoot dry weight and plant dry weight under two N conditions and their relative traits were used to evaluate low‐N tolerance at the seedling stage. A total of 44 QTLs were identified on chromosomes 1, 2, 3, 4, 5, 6, 8 and 9. Eight intervals on five chromosomes were identified to harbour multiple QTLs, suggesting pleiotropism or multigenic effects according to the contributor of alleles. Some QTL clusters were found in the nearby regions of genes associated with N recycling in rice, indicating that the key N metabolism genes might have effects on the expression of QTLs. Several unique QTLs for relative traits were detected, which suggested the specific genetic basis of relative performance.     

Marker‐assisted backcrossing of a null allele of the α‐subunit of Soybean (Glycine max) β‐conglycinin with a Chinese soybean cultivar (a). The development of improved lines

The development of soybean varieties that lack the β‐conglycinin α‐subunit is an attractive goal because the β‐conglycinin α‐subunit negatively influences the nutrition and gelation of tofu and is a major allergen. To remove this undesirable allergen and simultaneously improve the seed nutritional value and food‐processing quality, marker‐assisted background selection (MABS) was used in backcross breeding to incorporate cgy‐2, a null phenotype version of the gene encoding the β‐conglycinin α‐subunit, from the donor line ‘RiB’ into the genetic background of the Chinese cultivar ‘Dongnong47’ (DN47), a popular high‐oil superfine seed soybean cultivar from Heilongjiang Province, China. In each F₂ (F₂, BC_nF₂) generation of the breeding programme, the offspring that carried the introgressed cgy‐2 were identified by sodium dodecyl sulphate–polyacrylamide gel electrophoresis and rescreened by MABS using simple sequence repeat markers to accelerate recurrent parent genome recovery. Of the 49 advanced backcrossing breeding lines (ABLs), the three best lines, ABL1, ABL2 and ABL3, were selected from the BC₁, BC₂ and BC₃ populations, respectively. The ABLs were evaluated for desirable agronomic characteristics, yield‐related traits, amino acid composition, free amino acid composition and tofu‐processing quality in the mature seeds. All of the ABLs lacked the α‐subunit but grew and reproduced normally without deleterious effects on physiological processes such as seed development and germination. The free amino acid content of ABL1 was significantly higher than that of ‘DN47’, with arginine (Arg) being particularly enriched. Compared to the recurrent parent ‘DN47’, the total protein content of the three ABLs was higher, the amino acid composition of the seed proteins was markedly modified and the yield and hardness of the tofu that was made from the ABLs were significantly increased. MABS combined with stringent phenotypic selection in a backcross breeding programme is a feasible strategy for the genetic engineering of seed protein components to produce allergenic subunit‐deficient variant alleles.     

Detection of additive and additive×environment interaction effects of QTLs for yield‐component traits of rice using single‐segment substitution lines (SSSLs)

Additive effects (A) and additive‐by‐environment interactions (A×E) for five rice yield components were analysed using 20 SSSLs under mixed linear model methodology. Thirty‐one QTLs were detected. Different yield components have different QTL‐by‐environment (Q×E) interaction patterns. No A×E interaction effects were detected for the four QTLs for panicle number (PN). Four QTLs detected for spikelets per panicle (SPP) had A×E interactions. Five of seven QTLs detected for grains per panicle (GPP), two of 10 QTLs detected for 1000‐grains weight (GWT) and three of six QTLs detected for seed set ratio (SSR) showed significant A×E interaction. Most of these QTLs were distributed in clusters across the genome. The complexity of linkage and pleiotropy of these QTLs plus environmental effect may result in the diversity of the yield phenotype in the SSSLs. Only S19 exhibited a significant increase in yield with a predicted gain by 281.58 kg ha^?1. The results may be useful to design a better breeding strategy that takes advantage of QTL‐by‐environment interaction effects in each of the SSSLs.     

QTL mapping of adult‐plant resistance to stripe rust in a ‘Lumai 21 × Jingshuang 16’ wheat population

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a devastating fungal disease in common wheat (Triticum aestivum L.) worldwide. Chinese wheat cultivars ‘Lumai 21’ and ‘Jingshuang 16’ show moderate levels of adult‐plant resistance (APR) to stripe rust in the field, and they showed a mean maximum disease severity (MDS) ranging from 24 to 56.7% and 26 to 59%, respectively, across different environments. The aim of this study was to identify quantitative trait loci (QTL) for resistance to stripe rust in an F₃ population of 199 lines derived from ‘Lumai 21’ × ‘Jingshuang 16’. The F₃ lines were evaluated for MDS in Qingshui, Gansu province, and Chengdu, Sichuan province, in the 2009–2010 and 2010–2011 cropping seasons. Five QTL for APR were detected on chromosomes 2B (2 QTL), 2DS, 4DL and 5DS based on mean MDS in each environment and averaged values from all three environments. These QTL were designated QYr.caas‐2BS.2, QYr.caas‐2BL.2, QYr.caas‐2DS.2, QYr.caas‐4DL.2 and QYr.caas‐5DS, respectively. QYr.caas‐2DS.2 and QYr.caas‐5DS were detected in all three environments, explaining 2.3–18.2% and 5.1–18.0% of the phenotypic variance, respectively. In addition, QYr.caas‐2BS.2 and QYr.caas‐2BL.2 colocated with QTL for powdery mildew resistance reported in a previous study. These APR genes and their linked molecular markers are potentially useful for improving stripe rust and powdery mildew resistances in wheat breeding.