Combining higher accumulation of amylopectin, lysine and tryptophan in maize hybrids through genomics-assisted stacking of waxy1 and opaque2 genes

Waxy maize rich in amylopectin has emerged as a preferred food. However, waxy maize is poor in lysine and tryptophan, deficiency of which cause severe health problems. So far, no waxy hybrid with high lysine and tryptophan has been developed and commercialized. Here, we combined recessive waxy1 (wx1) and opaque2 (o2) genes in the parental lines of four popular hybrids (HQPM1, HQPM4, HQPM5, and HQPM7) using genomics-assisted breeding. The gene-based markers, wx-2507F/RG and phi057 specific for wx1 and o2, respectively were successfully used to genotype BC1F1, BC2F1 and BC2F2 populations. Background selection with > 100 SSRs resulted in recovering > 94% of the recurrent parent genome. The reconstituted hybrids showed 1.4-fold increase in amylopectin (mean: 98.84%) compared to the original hybrids (mean: 72.45%). The reconstituted hybrids also showed 14.3% and 14.6% increase in lysine (mean: 0.384%) and tryptophan (mean: 0.102%), respectively over the original hybrids (lysine: 0.336%, tryptophan: 0.089%). Reconstituted hybrids also possessed similar grain yield (mean: 6248 kg/ha) with their original versions (mean: 6111 kg/ha). The waxy hybrids with high lysine and tryptophan assume great significance in alleviating malnutrition through sustainable and cost-effective means. This is the first report of development of lysine and tryptophan rich waxy hybrids using genomics-assisted selection.

Genetic Similarity Between Donor And Recurrent Parents Can Reduce The Number of Backcross Generation In Marker-Assisted Backcross

The marker assisted backcross (MABC) method is the most used to obtain transgenic hybrid and transgenic inbred lines in maize with few backcrosses (BC) generations. It is possible that the use of donor parents with greater genetic similarity with recurrent parents can further reduce the number of BC generation to recover recurrent parent genome. The objective of this study was to evaluate the influence of genetic distance between parents and the percentage of recurrent parent genome recovery, as well as the similarity of BC plants and recurrent parent. Nine maize BC populations were evaluated, with genetic distances between donors and recurrent parents ranging from 0.238 to 0.499. In the backcross generations, molecular markers were used to identify the plants with the highest percentage of recurrent genome recovery and with greater similarity to the recurrent parent. There was no difference in the recurrent genome recovery among populations after three BC generations. In the first two BC generation the similarity between BC plants and recurrent parents was positively correlated with the similarity between donor and the populations recurrent parent. BC populations with higher similarity among parents could be finished with two BC generations, and BC populations with lower similarity could just be finished after three generation of MABC. The use of donor parents with higher similarity with recurrent parent can reduce one BC generation in MABC approach.

Enhancing backcross programs through increased recombination

Background Introgression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters. Results In this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental. Conclusions Depending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation.

Recovery of Recurrent Parent Genome in a Marker-Assisted Backcrossing Against Rice Blast and Blight Infections Using Functional Markers and SSRs

The most vital aspect of marker-assisted backcross breeding is the recurrent parent genome recovery. This enables the selection of only parents with recovered recipient/recurrent parent genome in addition to the targeted genes. The recurrent parent genome recovery (RPGR) ensures that non-desirable genomic segments are removed while the gene of interest is sustained in the recombined progenies without further segregations. This work was aimed at quantifying the RPGR of backcross populations with introgression of bacterial leaf blight resistance genes. Putra-1, a Malaysian elite variety, high yielding with inherent resistance to blast but susceptible to bacterial leaf blight (BLB), was crossed with IRBB60 which is resistant to BLB disease. The IRBB60 has four Xoo resistance genes—Xa4, xa5, xa13 and Xa21. Tightly linked polymorphic functional and SSR markers were used for foreground selection at every stage of backcrossing to select progenies with introgressed target genes. Background selection was done to quantify the percentage of RPGR in the selected lines using 79 confirmed polymorphic microsatellites. Result obtained showed that the percentage of RPGR was 80.11% at BC1F1, 95.30% at BC2F1 and 95.9% at BC2F2. The introgression of Xa4, xa5, xa13 and Xa21 Xoo resistance genes were faster through the adopted marker-assisted backcross breeding compared to what could be obtained through conventional breeding. All the 16 selected lines displayed resistance to BLB with three lines showing high resistance to the disease. The blast resistance contained in the genetic background of Putra-1 was also sustained in all the selected lines. The newly developed lines were recommended as new rice varieties for commercial cultivation.

Enhancing backcross programs through increased recombination

ABSTRACTIntrogression of a QTL by successive backcrosses is a strategy that can be used to improve elite lines (recurrent parent) by bringing in alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since one selects for the donor allele at the QTL, the elimination of the donor genome in the neighborhood of that QTL will be much slower (linkage drag). Using markers to monitor the genome around the QTL and in the background can accelerate the return to the recurrent parent genome. The success of an introgression will partly depend on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two aspects of recombination. Here, we assess, by simulation, their effect on the efficiency of introgression programs by studying the reduction of the linkage drag and the recovery of the recurrent genome. The selection schemes we simulate begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that when the QTL is in a region that was initially lacking crossovers, increasing the recombination rate can decrease the linkage drag nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region already rich in crossovers then increasing recombination proves to be detrimental.Key messageIn breeding programs, recombination is essential for introgression, but introducing more crossovers is beneficial only when the target is in a cold region, otherwise it is detrimental.