Inheritance And QTL Mapping For Earliness In Upland Cotton

Early-maturing germplasms are important genetic resources in Upland cotton breeding. In China, with the introduction and utilization of King’s cotton, a breakthrough progress has been made in early-maturing breeding, yet it also narrowed the genetic diversity, leading to the bad efficiency in the improvement of overall traits. Today, the narrow genetic bases has been the bottleneck for cotton breeding in cotton growing countries including USA, China, Australia, India, etc, so it is important to create and diversify the cotton germplasms. Currently, It is more and more difficult to improve yield of early-maturing upland cotton by conventional breeding, therefore, studies on the inheritance, quantitative trait loci (QTL) mapping, and genetic diversity for maturity are needed based on modern molecular biotechnology. Few studies have been reported previously on QTL mapping for earliness and its related traits in upland cotton. In this study, on the base of the genetic diversity analysis of different early-maturing upland cottons, QTL for earliness, yield and fiber quality traits were identified, and the heredity of these traits as well as their association analysis were carried out in order to serve the early-maturing upland cotton breeding.Forty-three early-maturing upland cotton cultivars were classified and compared according to their parental origins, breeding sites and trait performance. The results showed that in Yangtze River Valley, compared to varieties developed in other cotton growing areas, Xinjiang cultivars matured late with growth stage elongated, better fiber quality, more hot-season bolls and fruit branches, but with less pre-hot season as well as autumn bolls. Whereas in Northwest Inland, Xinjiang cultivars matured early with more pre-hot season, hot season, effective, pre-frost and total bolls, increased fruit branches, pre-frost seed cotton and lint yield, higher rate of pre-frost cotton, and better fiber strength and spinning consistency index. Among varieties derived from different ancestors, C42 and 611Bo performed early-maturity and had more pre-hot season and hot-season bolls; Deltapine and Uganda derived lines had more effective fruit branches and total bolls, and better fiber quality; Kings derived lines had a higher pre-frost seed cotton yield, lint yield and lint percentage; furthermore, the Kings, Tashkan as well as Uganda derived lines showed greater boll weight than others. One hundred and seventy-four polymorphic primer pairs were used to divide the 43 cultivars into 8 clusters, consistent with the breeding region, pedigree and genetic bases of these cultivars. Four hundred and eighty-six allelic variations were detected with 2.75 polymorphic loci per primer pairs and the polymorphic information content (PIC) 0.331. Though the number of alleles revealed by SSR primers had a huge range, the average number per chromosome was at a low level, indicating the genetic basis of upland cotton was narrow.Based on analysis of genetic diversity among 43 varieties, the level of linkage disequilibrium (LD) within the whole cotton genome was analyzed using TASSEL software. Results showed that though the LD sites had a huge number, their distribution was not uniform within the cotton genome. LD sites were concentrated on individual markers at chromosome All, D5 and D12. Three hundred and ninety loci associated with 12 traits were detected across multiple environments, of which 90 were highly associated. In combined analysis, thirty highly associated loci were identified. Five markers on D9, A2, D2 and D6, which were associated with flowering, growth stage, first fruit branch node and pre-frost bolls, were detected in multiple environments and in combined analysis respectively, suggesting the existence of QTL in these regions. Based on the allelic variation relationship between genotypes and phenotypes, several trait-associated loci as well as elite materials were identified. Positive alleles adjacent to NAU5467-1, NAU3519-2, NAU4048-1, NAU2687-2 and BNL1317-2 obviously shortened budding, flowering and growth stages; positive alleles near NAU5467-1 and NAU3519-2 dropped the first fruit branch node and its height; while positive alleles close to NAU437-1, NAU1366-2, NAU3052-2, JESPR291-2, NAU5379-2 and NAU462-1 increased pre-frost bolls, pre-frost seed cotton yield and lint yield. These positive alleles were from elite materials XinluzaolO and Jinmian14, which were derived from the former Soviet Union and King’s cotton respectively.6×(6-1)/2 crosses were made with six early-, mid-and late-maturing upland varieties (Xinluzao8,10, Ningzaol, Sumian12, Jing8891, TM-1). Based on data of parents and F1 in three environments, the gentic components of parents, favorable and unfavorable loci for F1 maturity and pre-frost lint yield heterosis were estimated by QTL detection system (ADE genetic model). The results showed that the phenotypic variations explained by major loci groups for maturity and pre-frost lint yield were 9.3～39.4(%) and 36.7% respectively. The additive effects of J=16 locus at budding, boll opening, and growth period were greater than other loci groups, suggesting that this locus had a key role in the early-maturity of upland cotton. Compared to late-maturing parents, early- and mid- maturing parents had less genotype and phenotype values at budding, boll opening, and growth period, and more favorable earliness related loci. In the major loci groups for pre-frost lint, Xinluzao8×Jing8891 F1 pyramided all favorable loci among the crosses. Besides, heterozygous loci contributed more to pre-frost lint yield than homozygous loci in most crosses. The yield heterosis of hybrids was mainly determined by heterozygous loci, though homozygous loci also made a contribution. These results also suggested the necessity to use local elite earliness cotton cultivars as core parents and traits with both high additive effects and high heritability as selection criteria in a cotton breeding program.Both F2 and F2.3 populations were made from the two crosses of TM-1 with Xinluzao8, Xinluzao10, respectively. Two earliness upland cotton genetic maps were constructed by JoinMap V3.0 based on SSR marker data, with a total length of 1284.88 cM and 598.14 cM, and 127 and 54 polymorphic loci, respectively, covering 11.97% and 25.7% of the cotton genomes. The average distance between two loci was 10.12 cM and 10.68 cM respectively. The first map included eighteen chromosomes, with three linkage groups unassigned; while the second map included 12 chromosomes. QTL tagging was performed using composite interval mapping (CIM) method of Winqtlcart 2.5. Totally 61 significant QTL with LOD scores greater than threshold value were detected for 34 traits including maturity, yield and fiber quality in the two populations. QTL clusters were found on D7, including 4 yield QTL simultaneously detected in the two populations. The QTL on A2 and D7 controlling growth period and pre-frost lint yield respectively were concurrently identified in association analysis, showing great stability. An integrated map was constructed through bridge markers, with 154 polymorphic loci distributed on 18 chromosomes and 3 unassigned linkage groups. The length was 1519.31 cM, covering 30.38%of the genome, with average interval between two loci 9.86 cM. QTLs for maturity, yield, fiber quality and other agronomic traits were detected on A2, A5, A6, A6/D6, A7/D, D1, D2, D7 and D9 respectively. QTL clusters were concentrated on D7, A6 and A6/D6. Favorable alleles were mainly from the two earliness varieties Xinluzao8 and Xinluzao10, which had genetic background of 611 bo and King’s cotton respectively. Earliness as well as its related traits was controlled by different genes, and additive inheritance is the major genetic base.